> that the compiler optimized away some 'empty' loops a little bit too aggressively without realizing that these loops were setting output pins.

Doesn't sounds like a bug in the compiler, sounds more like `volatile` was not used (unless, of course, `volatile` was not being honoured).

I still run across this to this day with GCC and Cortex-M code. The optimizer will occasionally decide to blow away loops that are clearly doing something.