Wow, this thread is full of all kinds of insanity. Why do people think making an MD5 checksum of a file means the file is "good or bad"? It all depends on what you're comparing against. There is no centralised source of truth for what makes a "good" or "bad" ROM image -- the GoodNES set is an attempt to do that, but it falls short. It's probably your best bet for comparison though.
Are you *absolutely certain* these problems don't happen on a real NES with the actual cartridge? It's the only way to be sure.
Re: climbing down a ladder: I can't reproduce this. I've made a video (requires XviD codec), ~2.3MB:http://www.malkavian.com/~jdc/indiana_ladder.XviD.avi
"Glitch on level 2 which makes Indiana fall through the floor" requires further information. Can you explain how to reproduce it? I can't even get to level 2 in this game (too lazy), so if you could put up a savestate somewhere, I'll take a peek. :-)