Look no further! I've found the culprit.
During my tests, I didn't notice I had EnableMipMaps set to 1 and that caused the problems I described in both games (though MipMapping was disabled in TR itself).
Oddly enough, my textures stay normal with EnableMipMaps=1, it's just that the TR inventory menu is light grey and the Redguard thumbnail snapshot is white (which made me think the transparency bug was creeping in again).
Since the default INI in the rc5 archive has EnableMipMaps=1, wouldn't it be safer to re-upload the library with a corrected INI file?
Anyway, rc5 gets my green light