That is incredibly weird. I've got more questions for you, if you don't mind, because I can't reproduce this at all.
* Can you consistently reproduce this?
* Was this a clean installation of CrystalDiskInfo Portable?
* Are you sure the theme folder never made it to App\CrystalDiskInfo\CdiResource on first run? I'm not doubting what you're telling me, I'm just hoping the theme folder took a little too long to copy (as opposed to not being copied at all).
* While CrystalDiskInfo Portable was running, did the theme folder get copied into Data\CdiResource\theme? (It's important that you check while CrystalDiskInfo Portable is running, because things change after the launcher exits)