In fact, I can reproduce that fact: MMV save states work in beta-3 but not the newest two builds. I found this bug and immediately related to it. Then, out of nowhere, keyboard shortcuts just stopped working. I couldn't determine exactly what was going on, but I knew that freshly created save states were failing to load on certain builds. Or maybe it was an issue with i686 or x86-64 specifically.
I thought maybe I was using an incompatible save state between versions. It seemed to save fine, but upon loading, it corrupted the game. Then I tried using save states in Mega Man V. When I first tested the latest builds, everything seemed to work - i distinctly remember using keyboard shortcuts for reset and pause. Let me take a few steps back and analyze what I did: Well damn, I also cannot seem to reproduce it anymore.