I think you would have to post your code to get a clearer picture of what you are doing.
the serial transmission stops when the speed of pulses increases
That could be for many reasons, do you know the frequency that this happens at? Is the ISR (Interrupt Service Routine ) taking too long? Is it printing a lot of data? Is the speed it happens dependent on the serial baud rate? Have you tried faster baud rates?
What arduino are you using, for example a Leonardo does not actually use the baud rate value in the serial port.