I've tried playing the 4.4 patch after building it, and I think I notice a minor bug has crept in.
When no weapon is equipped, collecting a weapon capsule should automatically fill the weapon with the lowest energy. I played up to Doppler Stage 3, and when I tried collecting weapon pickups in the teleporter room (from shooting the generator), they did not automatically refill my lowest weapon gague. No sound played, no weapon energy was gained. I had to have a weapon equipped for it to recharge it. I was on New Game Plus, playing as X with golden armor, with Zero defeated to get the Z-Saber.
What's interesting is that after beating the game, I loaded another save file on New Game Plus, and the energy balancer worked correctly. I also tried reloading the exact same save at the exact same stage, and that time I went through, it also worked correctly. It might have just been a one time fluke, or one of those bugs that's difficult to reproduce.