I also have this problem with my laptop, hp8540w.
The bios recognizes in the boot the two disks, the first one is ssd, and the second one is external esata. The first with the system always starts, the second data sometimes does not load at startup.
The airboot114 always shows both discs.
What works best is to turn off the laptop and unplug the esata along with the power USB with the notebook turned off, wait 10 seconds, plug it in again and turn it on.
Maybe it could be a problem of the shutdown, which never really turns off, does a reset.
saludos