I don't think that being on a separate partition would slow it down.  I think that if anything, it would make it a bit faster, since that partition is not being accessed as much as your primary one.  I usually try and keep my content all on a separate physical drive though.  Which is why I have like 10 physical drives in my rig lol..  Lot's of content.  Your issue might be a case of just a slow drive.  Sometimes a defrag can help speed things up, but not so much with Windows 7.  I don't know exactly what drive hardware you have so I can't give out more info.