I don't think that there is one single cause of all the issues that I'm seeing.
The G-6 has one working skin, I/Jg52, but it is the most recently updated one (I want to avoid comparing updates skins though for now). II/Jg27 has never been updated with a bump or spec map, so I'm not really worried about that one yet.
But my other four (including 9./Jg 54 seen in the screen shot), were all created the same time with bump and spec maps and they all have the same problem.
With the G-2 the only correctly appearing skin is the one seen here, Stab./Jg 77. One has been updated and is correct in AH2 but not in AH3: 9./Jg 52. The original had no bump or spec map but received both and a corrected paint job in an update. The paint job is updated, but I don't think the other files carried over because this skin has the normal map matching the default G-2 and not any of my 109's. 9./Jg52 should now have the same settings as Stab./Jg 77, but does not in AH3. (what is odd is none of the updated files for 9./Jg 52 are on the skin admin page)
G-6 I/Jg 52 (correct)
G-6 9.Jg 54 (incorrect)
G-2 Stab./Jg77 (correct)
G-2 9.Jg52 (incorrect)
9.Jg52 is consistent with skins that had no bump or spec map in AH2 - except this skin was updated with those files.