I had similar issues a while back, it was always image files that refused to delete from the trash, due to 'being in use'
It turned out to be Twitter for mac that was causing the issues. If I grabbed an image from say skitch or an image file I have dragged from a webpage to the desktop to post to twitter.
Quitting Tweetie and then emptying the Trash was the only way around it.
Seems you have sorted it now, but this is my only experience of the trash not emptying before.
C.