[Darkjedi]

Make sure that in E-mail setup under Advanced Settings, you select something to the effect of "Keep on server" under the "When deleting messages" drop down. It's the advanced settings on the Automatic Send/Receive schedule tab.

I've used imap on gmail with MR 6.1 and always had my messages deleted off servers. In fact I probably would've been peeved if the messages didn't reflect what I did on my phone as that's the main reason I use imap. I don't normally use POP3, but I'm pretty sure I've seen people use that option while using the POP3 protocol.