It looks like it's -still- not fixed. Darnit.
I'll try adding some timing elements; see if that's causing the problem - For some reason, the charging chip's mode is not set to whatever BME happens to want, and it complains.
edit:
I was told "Oh, yea, it's -perfectly- safe. I've been using it for weeks. Nothing to worry about." Yea...

One thing you can do to (possibly) fix USB mode is:
1. Open up a console, gain root.
2. type "stop bme", plug in your USB cable.
2. extract /usr/share/backupmenu/extrafiles.tar.gz
3. run "./bin/charge.sh" from inside it. Wait a few seconds for it to say "charging" etc.
4. hit ctrl+c to cancel it, wait 20 seconds until the LED goes solid orange.
5. Hit "start bme". Things should begin to charge normally and USB mode will work again.

edit: The above -may- not work above 90% charge; you may have to let it run down to around there, then try it. Why? I dunno.