I have come across this issue of nether my early 2011 MBPS 17 or my late 2011 Mini Server will boot under mountain lion if they have a thunderbolt cable connected too them. It makes no difference if you have a device on the cable or not they will not complete a boot cycle "the main screen comes up with the top menu bar and that's as far a it goes. If you disconnect the cable both machines will boot fine after whitch you can plug the cable in and any devices will been seen.
There has never been a problem with Lion but there is now under Mountain Lion. I also have an iMac 27" and that works fine with the cable and devices connect at boot time.
Has anybody else seen this problem ? One thing to note if you want to boot from a thunderbolt drive you if you hold down he alt key and then turn the power on.
Chales
