Fair enough- I'll do some homework (although I warn you- I've only basic experience with software language- and Java is a totally alien language to me):
Wait (from purely layman's testing)- the screenshot generally seems to work properly mostly, without touching the resize panel in any way..
Resizing and it's still working.

It's definitely a very vague circumstance that's causing the hickup.
A wild and totally uneducated guess is it might be the Injector, after maintaining a bigger log of all of the programs I frantically downloaded, possibly looked at (storing all data in a cache in case I bring it back up again), and starting to think it has to start going easy on memory to keep running at otherwise optimal level without straining the machine (most of these types of programs assume they're still in 1992, working on fragile machines on which display of plain-graphics could cause a crash, and therefore base performance and functions on REALLY low memory requirements- cutting frivolous excesses like pictures first when things look choppy).
Although I can't explain the resize-correction- it's probably that the window itself is itself, or referencing a separate program linking back to 'Windows' window program, and reloading all the data when making corrections using its own, separate processing functions from the Java ones...
Am I close?
Generally, the non-coverage issue is purely relating to maps I downloaded normally without the Quake injector.
Particularly, most of the Quoth maps I already had installed like Sickbase, Thehand etc don't show as being ticked in the injector. Maps I installed (or reinstalled) via the Injector always show.
And I was afraid you would be saying that about Darkplaces.

I'll try it out manually with Fitz.