I would put the original video card back in the DZ68BC, and buy another low-profile card for your other system.
I are right about the risk with upgrading to BIOS. BIOS 0028 is the best for Sandy Bridge (based on my personal experience, and once upgraded there is no way back..). The release notes of BIOS 0039 also don't show any special fix for external video cards.
I guess it's just luck of the draw. Even the other slot didn't help, but the card isn't actually bad, since I tested it in an unrelated system. Oh well. Not that Intel is updating the BIOS for this board anymore, but it would have been nice if this Sandy Bridge/Ivy Bridge BIOS split never happened. I never really got to update it again after the initial flash a couple years ago.
FYI: There is a new BIOS version (fixes the "unsupported CPU screen at startup), but you need to contact Intel support for it as it is not published. BIOS 0028 is still better for Sandy Bridge.