I've got the exact same problem... boot from a power off state, and it boots right into ALARM.... issue a reboot command, and it boots PogoOS... This is on an original pink pogoplug v2
I'm booting from a flash drive with an ext2 boot partition and an ext3 system partition in the front USB port, and a USB hard drive for storage on one of the back USB ports... so I don't think its a HDD spin up issue, as boot and system are on a flash drive.
I'd love to get this resolved... its a complete P.I.T.A. to have to go and pull the power plug instead of just being able to "shutdown -r now" or "reboot" anytime I need to reboot the system....
