I've never had that problem before. How far into hacking SMW are you? I think you should use the Clean ROM verifier on the original SMW ROM you downloaded to see if it's clean. I don't think any patches here would ruin Mario's palette, but then again, using too many patches isn't recommended because some of them conflict with each other. If it's a dirty ROM, there are other places where you can get a clean one, but posting links on this forum is forbidden.
(Edit: When I asked how far into hacking you were, I intended to find out if it was caused by something other than a dirty ROM, like a faulty code that may have overwritten something, but yeah. You can move levels and palettes from a dirty ROM to a clean ROM without issues.)
Just look above you... If it's something that can be stopped, then just try to stop it!
Here' the link: http://s228.photobucket.com/albums/ee260/daboys121/?action=view¤t=messedupMario.jpg
I don't like small Mario but I like big Mario which is here: http://s228.photobucket.com/albums/ee260/daboys121/?action=view¤t=SuperMarioWorld_00002.jpg
I drew angry eyes on Mario.
I'm not too far in my hack. I could start over, but it would be very annoying.
Here's an idea.
Use a new copy of your SMW clean rom, and transfer all the levels and stuff over, except Mario's pallette.