I use Paint Shop Pro and sometimes Gimp. I think it has more to do with using DXTBmp properly. I use RSBin Tool to convert to dds and back. Rarely use RWTools for paint work. Hope that helps.
1. Open file with RSBin Tool
2. Export dds
3. Open dds with DXTBmp
4. Export main file to PSP and edit then export the alpha to PSP edit and save. DXT will show both the main texture and the alpha at the same time in two windows for editing.
5. Import saved dds back into RSBin Tool. Save.