I am in the same case.
Installing lenny, upgraded to debian squeeze 8 worked fine. Tried all the usb slots, perfect. Move to the hdd to anoher dockstar, no proble at booting.
I decided to clone my boot partition to compact flash. I failed to clone it to smaller volume. So I decided to install lenny to CF from scratch.
Setup worked fine. But after reboot, It always goes to pogoplug prompt, for any of my both dockstar.
I though it was bad installation and retried to install from scratch, 3 or 4 times with no success.
I pu put the hdd back in place of CF and DS booted immediately.
So what is the issue with compact flash in multicard reader? If you have any idea, just tell us the working tip.
Thank you ;)