Alpha and FFv3R

[daglob]

When I've converted some files with alpha channels, there were no problems. When I converted others (female cape, for instance), the "invisible" section aren't invisible anymore. Re-converting or re-saving the files at 32 bits doesn't seem to work. Others (PV_Clark Kent), the entire alpha'ed section (Kent's glasses) are missing.
Any idea what I'm doing wrong?