Yes. Anything to do with the timers can be different on the two processors.
Also look at memory the Leonardo has more SRAM so code could run out of memory on the UNO where as it would not on the Leonardo. Look at the compile output to see how much each is using as a percentage of the total. Running out of memory would cause erratic behaviour like you describe.
I would suggest this has nothing to do with the computer you use to program the two processors.