Forwarding an email does change things like headers etc though doesn't it?

I do the POP3 from a gmail (with my name) to my Google Apps account in my own domain i.e. exactly like you want to do.

If you go to settings Acccounts tab where the POP3 account is set up does view history tell you anything?

I didn't have to adjust that setting I don't think. It could be your problem. I presume it's something like unencrypted POP3 vs encrypted (POP3S or STARTTLS)?