On the PC are you using a desktop client like Thunderbird or Windows Live Mail or some other? If so, it sounds like you have the account configured in the client using POP3. If that is the case, the client will download the emails and then delete them from the server by default unless you set it not to do that. The phone would then not "see" the messages on the server anymore. If you are going to access your email from multiple devices, the best protocol to use is IMAP. That way everything is synced.