This is an odd issue, and I would like to know how to troubleshoot it.
I recently updated to 4.6.8 and I now it will randomly boot into the second drive instead of the first. It once booted into the second drive with me manually selecting the first drive via F10 but I haven't been able to replicate that. I can replicate it booting the second drive if I reboot a few times.

It's set to boot to SD card, but will occasionally boot to mSATA.