That's just still. There's no reason the Wordprefect files cannot be used to make the eBooks. In fact, Word would read them. Sure, thee could possibly be some formatting issues in the conversion, but nothing major and nothing that can't easily be fixed. If I was working at S&S, I'd be embarassed to think the eBook staff was that untrained and didn't know how to do it.
Okay, maybe that's not the problem. That was just speculation on my part. I've never actually discussed this with anyone at Pocket.
It very well could be the problem. The problem could be they won't or don't want to go the extra step to convert.