I forget the details of the Pro-1000 driver as I no longer have the printer, but if it allows to set BOTH the paper thickness and the platen gap try increasing both. It won't affect print quality. From one interpretation of what you describe, I'm wondering whether there is a bit more than usual paper curl at the end of your sheets. This can happen, and with relatively thick media create such an issue. Check for curl and if you see any, try bending it backwards without creasing the paper before you feed it into the printer. A problem with the vacuum system is less likely to be the issue from what you are saying.