That's a new one to me. I know that once you get to a certain level on basic (13 I think) you stop receiving rep, but I've never heard of a case where you actually lose rep. If you are sure that you were a higher level before your break, like everyone above mentioned, I suggest contacting Disney about the matter.
Here is a contact page on the Pirates Online website:
http://piratesonline.go.com/#/help/contact_us.html