Hi Jim,
All I'm running is GWX 2.1 (with the Minor Fixes released by BBW) plus my Ubermod, which basically has new scene.dat, envcolour.dat(s), skycolour.dat(s) files, plus tiny tweaks to the GWX 2.1 materials.dat and particles.dat files, and of course my GUI. That's it - no ships added or modded.
Here's a Medium Cargo with no flag. Would have been better if I had snapped the shot quicker (while the eventcam was to the side of the ship) but you can see even in this shot that the flag is missing. For comparison, there's a museum shot of the same ship (
with a flag) below it.