Serial communication and interval timer integration problems

You have 50000 clocks there.

What you can't see is the delay between the timer hitting its count and the cpu performing the first IORD/IOWR.

It is likely to be the same for every expiry - so everything will look fine - until your ISR processing takes all the cpu time.

IORD/IOWR themselves are likely to be 3 clocks (plus time to get the data to write, and fetch any code from external memory if you aren't executing from tightly coupled instruction memory and the code isn't still in the cache), but the time to save the registers and then call your ISR is a lot.