When you right-click the Deleted Items folder, a drop-down menu ought to appear, one of the items on it being Empty Folder.
Is this happening? If it is, does it clear everything out of it? If you empty the folder using the iPad, does stuff disappear properly?
If stuff is syncing back to your iPad, it sounds like you are using IMAP, or possibly Hotmail, for which MS provide their own connection scheme, also used with MS Exchange servers.