I noticed that my POP retrieval option works, but I do NOT have the "leave on server" box checked and it still leaves it on my original server. I only noticed this when I stopped getting email and went to my host ISP to find out that 1000's of emails were sitting there. All of those emails were already Popped to my Spamcop account.

How can I insure that my mail gets deleted from my original server after it is Popped to Spamcop?

Thanx

First thought might be to go through and change a few settings, diddle around a bit, come back and toggle them to what you really wanted, and give it a shot. Maybe just a "refresh" of some of these bits will solve it? You didn't say how far back the "undeleted" messages dated to, so not sure if the recent crash may have had an impact, for instance.

Apparently something has changed, the question is what and when?

stopped getting email - not sure exactly what you mean by this as you also say, 'All of those emails were already Popped to my Spamcop account"
If you could explain this a bit more clearly it might shed some more light on the subject.

You might also ask the provider of that POP account why this might be happening and what they might be able to do (or help you do) to fix it.