I setup my Gmail on my device. If I read it on the BlackBerry it shows up as read on my desktop which is the expected behaviour but when I read the message on my desktop, the message shows up as unread on my BlackBerry. I searched but can't find a fix for this.

I'm also on the BES for my corporate account and don't have this problem.

This is working normally. You can't find a fix because nothing is broken.
GMail does not have two-way message reconcilation.

BES does.