Ok, for one thing, practically nothing works correctly, like ledge jumping, any of the solids, etc. Only ice and falling in holes appears to work properly. I think Link's sprites for walking up and down need to have their origin fixed as well or they just need to be centered or something (left and right animations seem fine), but the sprites aren't what is causing the problem.
I think you just messed up some of the original engine somehow. I'm not sure if you did copy and paste and just missed some stuff or what, but it's clear that some key mechanics are screwed up. I'll check it out some more and see if I can figure it out. I'm gonna download the MC Engine again if I can find it, and I should be able to help then. That is, if no one else helps first.
Huh, the search finds nothing??? It didn't even find anything by searching for "engine"... What's up with that? So yeah, I can't find the MC Engine, but Diminish just posted below (as you can see) and he obviously knows more about it than I do, so no worries I guess.