Single step debug and timer's counter value
This sort of detail varies considerably between microcontrollers.  This specifically has to do with how exactly debugging and single stepping is implemented.

Manufacturers don't want to add a lot of hardware just for debugging, because that burdens the case where a large company wants to buy 100 k pieces at a time for a production run.  As a result, all kinds of clever schemes exist for re-using existing hardware.  One common scheme is to have the part execute special code to help implement the debugging interface.  To the processor, this is just code, so counters and the like keep running.

The switch to stop the counter during single stepping in your case probably only means the peripherals are shut off when the chip is idle, not when the debug code is running and communicating with the debugger.  It may be in your case that this debug code takes 15 cycles per single step.