Ah, err... Woops, he he, my fault I'm afraid :)
Easy fix: delete user_theme.xml. It'll work just fine. This is the old format, I'm quite surprised that the latest muCommander build accepts it, actually. There's something dodgy going on there.
I'll look into it, but in the meantime just delete the file and restart muCommander. Once that's done, if none of the predefined themes suit you, I'd suggest copying mucommander.jar/themes/ClassicCommander.xml as the user_theme.xml and manually tweaking the file. The current UI works, but doesn't offer nearly enough customisation power. We'll be updating that next, but for the moment power users are advised to edit the xml file by hand.