If I understand correctly, your stimulus program does the processing it needs to do and then waits for the trigger from the scanner, at the start of the next volume. Also, the scanner triggers are being received by your program as "6" key presses. If that is all correct, then I think the most likely problem is that your program is occasionally taking more than a TR to do the needed processing, so it then misses the trigger. You could try increasing the TR a bit, to see if the problem goes away. If it does, then you need to make your code more time efficient for it to work at your desired TR.

You could also check to see if you computer is really receiving all of the stimulus triggers. To do this just, open Matlab but don't start your stimulus program. Then run the your fMRI pulse sequence and see if the appropriate number of sixes appear in the window. If too few sixes appear then you probably have either a setting or hardware problem with the components handling the ttl signal and converting it to a 6 press.

Good luck

Thank you very much. I will try your advices and let you know the result

Best regards