So in trying to investigate a bit further; My steam controller only has inputs recognized by the game as Return, Enter, F9, F7, and the up, down, left, right keys.
Conversely, my 8bitdo controller, even plugged in via USB is recognized without a mapping for switch, menu, pageup, pagedown, and start/select (I think that is Home and End).
Using a remapper like Antimicro did nothing to change the behavior of these mappings, nor did changing the launcher presets; 1998, STD gamepad, steam original, all behaved exactly this way.
The WEIRDEST thing is that initial load of 7th heaven 2.0 about two months ago worked with overlay issues on only the launcher, and now, the application seems to break it's connection to steam on load, forcing a pop-up from UAC at start. That may be my machine and not the application, however. Will try changing administration permissions and try to get the mappings to apply this way.
ANYWAY, my guess is that the launcher thinks that these controllers are something other than controllers and is enforcing mappings on load that would work like another device.
Super weirdness.