Thank you. It looks like a problem in Img2Tex, it is not always converting the alpha correctly. That is why 24-bit fixes it (but then I think maybe there is no alpha? which is OK for some images, but not for others that need it!).
Anyway, first version of my tool:https://mega.co.nz/#!IRIRjJaL!SueuJCQNn6n-X-GZ2ucq8R-NWzo67wJC2s4sG-qX0IA
How to use:
1) First select the source files to convert (e.g. all the battle textures). So extract them from the LGP file first if you haven't done this yet.
Then select an output folder. Could be the same as the folder with the TEX files in it, or a different folder.
Click 'Convert TEX->PNG'. The output files will be named same as input files with '.png' on the end, e.g. oqac -> oqac.png
2) Once you have edited the PNG files, go back to the program, and this time select the PNG files as the source files. Choose an output folder to put the new TEX files in. (It will overwrite any files already in this folder). Click 'Convert PNG->TEX'. This time it removes the '.png' from the filename, so file 'oqac.png' -> 'oqac'. (So if you have not changed the filenames from step 1 above, this should be fine!)
So far I only support 24-bit and 32-bit PNGs - I think that if you are going for increased quality, you will probably not be using 8-bit?
I have tested editing a few textures (& increasing the size!) and it worked OK for me. I expect you may find some other problems too when you try it though, please let me know