A point of clarification:
... but none of the clones are actually bootable (go into BIOS and choose the newly cloned drive as boot disk).
Are you saying you're trying to boot your system when both the original and clone are connected?
Just wondering because over the years I've always had mixed results doing that, (ie. you essentially have two identical HDDs connected to the system), so much so that the original is now always disconnected, (pull the data cable), when I've cloned a HDD and want to boot off of it.