Maybe the TGAs have to be in 24-bit format? I'm not sure about this, but I distinctly remember them having to be 24-bit for something in RTW... Ah yes, it was for Alpaca's height generator program, before its fix in 1.5/1.6, where the map TGAs had to be in 24-bit format or they wouldn't work. But if you replaced them with vanilla GUI files... hmm, then I don't know. But I do recommend trying all new modding additions on a vanilla copy each time, as that helps isolate the problem... although you probably know all this far better than I.