Wasn't it supposed to self tune for max HR based on feedback from the on-die temp sensor, or am I imagining things again?
The temp sensor does work, check out the cgminer output instead of the (filtered) webinterface.PS: I'm thinking that the first device hashing at.... 12 Mh (lol) is the CPU of the Raspberry Pi... 
The 1st device is also the BabyJet. You probably unplugged the usb cable and plugged it back in when cgminer was running or something.