In my case : "unable to initialize libusb: -99?" .
Also, I reboot or shutdown nicely, and leave the system time to do it's shutdown (maybe including some remounting I seem to recall) until it's in "halt", and I use the Adapteva supplied supply, but sometimes there's a serious file corruption preventing it from starting up, and requires the rewriting of the card. Really annoying, thus far unpredictable, and in some cases can be helped by letting a Linux machine (fschk) correct the file system, the computer then finds errors, corrects them an in all but one or two cases, the Parallella will boot up again. If it doesn't, it gets stuck with some file error before loading the kernel or something, then it's pretty dead. Anyone else had this experience ? I've got a Raspberry PI too, and never had an error with the card or a problem starting up, also a HD video cam with card never has any problem at all..
T.