I've done all these suggestions (long ago) but continue to have the problem.
However, I have found how to always have the problem and how to always not have the problem. (Sorry for the split infinitives! ;-) )
If I have email "A" selected (open in a separate window or not), then clicking on email "A"'s delete "X" almost always does nothing. Also, if I try to drag the email to another folder, a copy appears in that folder but the original remains in the inbox.
If I want to delete email "A" and I have a different email selected (open in a separate window or not), then clicking on the delete "X" for email "A" will always delete "A".
Can anyone else confirm if your problem reacts the same.
Thanks,
Stan