diff --git a/artiq/coredevice/comm_generic.py b/artiq/coredevice/comm_generic.py
index a737dfb84..88fee184b 100644
--- a/artiq/coredevice/comm_generic.py
+++ b/artiq/coredevice/comm_generic.py
@@ -95,7 +95,12 @@ class CommGeneric:
     def _write_header(self, length, ty):
         self.open()
         logger.debug("sending message: type=%r length=%d", ty, length)
-        self.write(struct.pack(">llB", 0x5a5a5a5a, length, ty.value))
+        self.write(struct.pack(">ll", 0x5a5a5a5a, length))
+        if ty is not None:
+            self.write(struct.pack("B", ty.value))
+
+    def reset_session(self):
+        self._write_header(0, None)
 
     def check_ident(self):
         self._write_header(9, _H2DMsgType.IDENT_REQUEST)
@@ -125,9 +130,8 @@ class CommGeneric:
         if ty != _D2HMsgType.LOAD_COMPLETED:
             raise IOError("Incorrect reply from device: "+str(ty))
 
-    def run(self, kname, reset_now):
-        self._write_header(len(kname) + 10, _H2DMsgType.RUN_KERNEL)
-        self.write(struct.pack("B", reset_now))
+    def run(self, kname):
+        self._write_header(len(kname) + 9, _H2DMsgType.RUN_KERNEL)
         self.write(bytes(kname, "ascii"))
         logger.debug("running kernel: %s", kname)
 
diff --git a/artiq/coredevice/comm_serial.py b/artiq/coredevice/comm_serial.py
index 691b43928..25c926a25 100644
--- a/artiq/coredevice/comm_serial.py
+++ b/artiq/coredevice/comm_serial.py
@@ -19,6 +19,7 @@ class Comm(CommGeneric, AutoDB):
             return
         self.port = serial.serial_for_url(self.serial_dev,
                                           baudrate=self.baud_rate)
+        self.reset_session()
 
     def close(self):
         if not hasattr(self, "port"):
diff --git a/artiq/coredevice/core.py b/artiq/coredevice/core.py
index 6923b8ce9..61e7ed353 100644
--- a/artiq/coredevice/core.py
+++ b/artiq/coredevice/core.py
@@ -116,7 +116,7 @@ class Core(AutoDB):
         binary, rpc_map, exception_map = self.compile(
             k_function, k_args, k_kwargs)
         self.comm.load(binary)
-        self.comm.run(k_function.__name__, self.first_run)
+        self.comm.run(k_function.__name__)
         self.comm.serve(rpc_map, exception_map)
         self.first_run = False
 
diff --git a/artiq/gateware/rtio/core.py b/artiq/gateware/rtio/core.py
index 9aad47127..ffe3a978f 100644
--- a/artiq/gateware/rtio/core.py
+++ b/artiq/gateware/rtio/core.py
@@ -44,7 +44,8 @@ class _RTIOCounter(Module):
 
         # # #
 
-        self.sync.rio += self.value_rio.eq(self.value_rio + 1),
+        # note: counter is in rtio domain and never affected by the reset CSRs
+        self.sync.rtio += self.value_rio.eq(self.value_rio + 1)
         gt = _GrayCodeTransfer(width)
         self.submodules += gt
         self.comb += gt.i.eq(self.value_rio), self.value_sys.eq(gt.o)
diff --git a/artiq/test/coredevice.py b/artiq/test/coredevice.py
index 1be60a398..0c5c32990 100644
--- a/artiq/test/coredevice.py
+++ b/artiq/test/coredevice.py
@@ -147,6 +147,33 @@ class SequenceError(Experiment, AutoDB):
         self.ttl_out.pulse(25*us)
 
 
+class TimeKeepsRunning(Experiment, AutoDB):
+    class DBKeys:
+        core = Device()
+        time_at_start = Result()
+
+    @kernel
+    def run(self):
+        self.time_at_start = now_mu()
+
+
+class Handover(Experiment, AutoDB):
+    class DBKeys:
+        core = Device()
+        t1 = Result()
+        t2 = Result()
+
+    @kernel
+    def get_now(self):
+        self.time_at_start = now_mu()
+
+    def run(self):
+        self.get_now()
+        self.t1 = self.time_at_start
+        self.get_now()
+        self.t2 = self.time_at_start
+
+
 class CoredeviceTest(ExperimentCase):
     def test_rtt(self):
         self.execute(RTT)
@@ -192,6 +219,21 @@ class CoredeviceTest(ExperimentCase):
         with self.assertRaises(IOError):
             self.execute(Watchdog)
 
+    def test_time_keeps_running(self):
+        self.execute(TimeKeepsRunning)
+        t1 = self.dbh.get_result("time_at_start").read
+        self.dbh.close_devices()  # a fortiori the core device connection
+        self.execute(TimeKeepsRunning)
+        t2 = self.dbh.get_result("time_at_start").read
+        self.assertGreater(mu_to_seconds(t2 - t1,
+                                         self.dbh.get_device("core")),
+                           1*ms)
+
+    def test_handover(self):
+        self.execute(Handover)
+        self.assertEqual(self.dbh.get_result("t1").read,
+                         self.dbh.get_result("t2").read)
+
 
 class RPCTiming(Experiment, AutoDB):
     class DBKeys:
diff --git a/soc/runtime/ksupport.c b/soc/runtime/ksupport.c
index a2eb090c6..032fe88ec 100644
--- a/soc/runtime/ksupport.c
+++ b/soc/runtime/ksupport.c
@@ -79,7 +79,7 @@ long long int now_init(void)
 
     if(now < 0) {
         rtio_init();
-        now = 125000;
+        now = rtio_get_counter() + 125000;
     }
 
     return now;
diff --git a/soc/runtime/main.c b/soc/runtime/main.c
index fec357a0f..41433d264 100644
--- a/soc/runtime/main.c
+++ b/soc/runtime/main.c
@@ -151,16 +151,18 @@ static void regular_main(void)
 
 #else /* CSR_ETHMAC_BASE */
 
-static void reset_serial_session(void)
+static void reset_serial_session(int signal)
 {
     int i;
 
     session_end();
-    /* Signal end-of-session inband with zero length packet. */
-    for(i=0;i<4;i++)
-        uart_write(0x5a);
-    for(i=0;i<4;i++)
-        uart_write(0x00);
+    if(signal) {
+        /* Signal end-of-session inband with zero length packet. */
+        for(i=0;i<4;i++)
+            uart_write(0x5a);
+        for(i=0;i<4;i++)
+            uart_write(0x00);
+    }
     session_start();
 }
 
@@ -181,7 +183,8 @@ static void serial_service(void)
         if(r > 0)
             rxpending = 0;
         if(r < 0)
-            reset_serial_session();
+            /* do not signal if reset was requested by host */
+            reset_serial_session(r != -2);
     }
 
     session_poll((void **)&txdata, &txlen);
@@ -191,7 +194,7 @@ static void serial_service(void)
         session_ack_data(txlen);
         session_ack_mem(txlen);
     } else if(txlen < 0)
-        reset_serial_session();
+        reset_serial_session(1);
 }
 
 static void regular_main(void)
diff --git a/soc/runtime/rtio.c b/soc/runtime/rtio.c
index 0e5cdad10..3329019ba 100644
--- a/soc/runtime/rtio.c
+++ b/soc/runtime/rtio.c
@@ -14,4 +14,3 @@ long long int rtio_get_counter(void)
     rtio_counter_update_write(1);
     return rtio_counter_read();
 }
-
diff --git a/soc/runtime/session.c b/soc/runtime/session.c
index 352bca791..1a7f5d879 100644
--- a/soc/runtime/session.c
+++ b/soc/runtime/session.c
@@ -70,11 +70,13 @@ void session_start(void)
     memset(&buffer_out[4], 0, 4);
     kloader_stop();
     user_kernel_state = USER_KERNEL_NONE;
+    now = -1;
 }
 
 void session_end(void)
 {
     kloader_stop();
+    now = -1;
     kloader_start_idle_kernel();
 }
 
@@ -189,10 +191,7 @@ static int process_input(void)
             }
             buffer_in[buffer_in_index] = 0;
 
-            if(buffer_in[9])
-                now = -1;
-
-            k = kloader_find((char *)&buffer_in[10]);
+            k = kloader_find((char *)&buffer_in[9]);
             if(k == NULL) {
                 log("Failed to find kernel entry point '%s' in object", &buffer_in[9]);
                 buffer_out[8] = REMOTEMSG_TYPE_KERNEL_STARTUP_FAILED;
@@ -311,6 +310,9 @@ int session_input(void *data, int len)
             /* receiving length */
             buffer_in[buffer_in_index++] = _data[consumed];
             consumed++; len--;
+            if((buffer_in_index == 8) && (get_in_packet_len() == 0))
+                /* zero-length packet = session reset */
+                return -2;
         } else {
             /* receiving payload */
             int packet_len;
@@ -465,12 +467,14 @@ static int send_rpc_request(int rpc_num, va_list args)
 /* assumes output buffer is empty when called */
 static int process_kmsg(struct msg_base *umsg)
 {
-    if(user_kernel_state != USER_KERNEL_RUNNING) {
-        log("Received message from kernel CPU while not in running state");
-        return 0;
-    }
     if(!validate_kpointer(umsg))
         return 0;
+    if((user_kernel_state != USER_KERNEL_RUNNING)
+      && (umsg->type != MESSAGE_TYPE_NOW_INIT_REQUEST)
+      && (umsg->type != MESSAGE_TYPE_NOW_SAVE)) {
+        log("Received unexpected message from kernel CPU while not in running state");
+        return 0;
+    }
 
     switch(umsg->type) {
         case MESSAGE_TYPE_NOW_INIT_REQUEST: {