It isnt a bug in the game. Its intentional. The fire from the seahorses (Lindas as we call them) is a set pattern upon entering the zone. If you up a back to the start of the zone the patterns of the fire will most likely change. This is the same for boss patterns. When doing an up a or dying the boss pattern will change.

I started with Nestopia when I joined the community. So there is no issue there. You will find a timing delay between your pressing the button and samus action on screen with the emulator. With original hardware and a crt there is no delay. But your runs won't be rejected just because they are an emulator.

As far as I know, all emulators are allowed that are under the drop down menu for submission. Frame rates should be close to 60 fps to mirror the NES. What kind of frame rate is your emulator putting out and what emulator is it?