It sounds to me like you set his "ignore solid" flag, am I right?
Not entirely sure how it could be useful, but perhaps you could have something with a platform in the middle of solid tiles and then boundaries at the bottom and top of Tile 44.. I can't really recall if that would work though.
If you can think of a good way to use it, go ahead, I'm not sure if it really requires assembly.
Oh, I just use to screw around a lot with what I did know.
That was really only situational, I just used what I had to figure it out.
I honestly don't know what all those numbers mean specifically in the game, I just used Translhextion, my favorite Hex Editor, to compare two copies of Cave Story, one original and one touched by the npc.tbl editor.
All of the differences it found obviously had to be where the corruption was, and a few copy/paste tests showed that I was right. If I wanted to use the npc.tbl editor, I just had to make sure to copy that bunch of code over again to remove the corruption.
That was more simple logic than code knowledge.
That would most likely be the cause of slight npc.tbl corruption, apparently because of the new CE, I haven't noticed myself yet, but it use to be a problem with Wedge's npc.tbl editor, and a rather shabby do-it-yourself quick-patch method was discovered, if you haven't figured out another way to avoid it yourself.
Sounds like his hitbox got screwed up with the npc.tbl corruption, allowing him to force himself through the ground, and since his stomp attack requires him to float directly above your position, he was able to re-orientate himself in the way you saw.
If you wanted to start changing any enemy behavior at all, let alone bosses, you'd want to start learning Assembly, which is the only real way to edit such factors of Cave Story. It's a very low level language, somewhere just above Machine Code, so I've found it hell to read and learn. I doubt I could help you very much at all, but Noxid seems to have memorized the stuff forwards and backwards, and has done some advanced stuff like custom TSC commands for me through Assembly, so you'd be better off asking him.
I got it to work. The problem was that I was naming them 1041 because of how the instructions were worded. Thank you so much, though; without your post I wouldn't have been able to figure out what I was doing wrong, so in the end, you DID solve my problem.