UPDATE: Just before leaving for work I tried PinballX database, as per scutters suggestion. That was correctly identifying present and missing media (as was Game Manager to be fair). In database there is a box to "hide backglass in game" which I checked. I saved the database when prompted and closed program. Restarted PinballX and tried to take a screenshot of a backglass with a set .res that PinballX would stretch out to full screen if saved thru B2s server. But this time Bingo! It took the screenshot with no issues.
I will try more tonight as I have a few to do. But seems like the hide backglass buttons are having a differeing effect between programs? Or maybe a glitch somewhere ironed out when the database saved?