How many files are you downloading at once? Reduce the number a bit. If you're resuming too many incomplete downloads it can cause problems...just resume a couple at a time.
Try disabling ultrapeer capabilities (tools > options > speed) & also disable any iTunes sharing options that you're using. You could also reduce your upload & download bandwidth a little & see if that helps.
Also try the tip below (click on link)

Tip: Purge the Downloads Queue!