I've seen bugs that presented like that.
For me it was extra mcu instructions, preventing a race condition or hidding atomicy issues
Good luck.
Discussion
The first thing a friend said was "That sucks. Race condition." I wish they were wrong.
I'm just going to keep it at debug logging for now. I don't want to take on development of yet another project. I don't have time to get to know another code base. I struggle to keep up with what I contribute to now as it is.
Sounds like the right call it's working, and not your codebase. time critical stuff can be a nightmare.