I looked at BetterScanning site and see a fixed height holder that has been discontinued and a variable height version as the current one available. You did not state which holder you have and it may not matter.
Put your Epson holder and BetterScanning holder together as if they were one holder positioned as they will be when on the scanner for scanning, any physical differences in any of their dimensions?
Somewhere in the settings of EpsonScan Pro screen is a pesky check box for auto marquee, deselect it and manually set the marquee to the frame. I have had problems with the auto marquee clipping usable image area in the past.
There is also the image frame selection on one of the tabs available via the Configuration box at the bottom of the Pro window, ensure the correct size is selected.
My scanners are not currently connected to the computer and I'm working from memory. I have a V500 and a V700.