OK, since nobody seems to know how to fix this, is it safe to delete my meatboy content, and reinstall? Will my saves be OK, and if no, where are they located so I can back them up?
C:\Program Files\Steam\SteamApps\common\super meat boy\UserData
(on my pc at least, check where your Steam install is gone and go from there)
^is where the SMB save game, backup and replay data should be. Back it up online if you want to be safe, by using Google Docs or Dropbox, for instance.
The load time between levels has been a bug in an older version of SMB, but it's not occurring for me anymore, so I can't help you there. Reinstalling the game data is always a good idea.