I made a test with my C7042 and i don't have any problem, maybe i miss something in your explanation:
driver made a track call (i set the track call to stop the cars) , i push the car#1 over the sensor and on my side PCLC just add a lap for car#1 and display the flag +1 and after i can end the track call by pushing again LC+BRake on the hand controller.
If i do the same with the track call option set to "pause the race", i don't have any problem: after the track call i push the car over the sensor and i can restart the race without any problem.