i had an issue that sounds like this as well where meat boy was constantly squishing on the ground, mainly in certain early warp zones. Supposedly you can fix that by using the detail launch options here http://supermeatboy.com/forum/index.php/topic,97.0.html

I was already using those just to make sure there werent any issues but i guess it ran to fast. It stopeed happening to me when i disabled -lowdetail options which i had previously enabled. (even ran fine for me on -highdetail)

Though i also hear controllers outside of the stock wired 360 one have compatibility issues so there is a decent chance it could be that too.

I had an issue that sounds like this on Win xp. What i did...

1) Used steam to verify the integrity of the game cache.
2) found supermeatboy.exe and tried to run as admin
3) came up with an error about "xinput9_1_0"
4) Googled "xinput9_1_0.dll", looked at results of people w/ similar issues, and downloaded the (apparently) missing dll
5) Put the dll in my system32 folder
6) Everything worked fine.

Good luck.

^^^
because of this:
http://supermeatboy.com/forum/index.php/topic,1959.0.html

Controller.