There is a new version of the unlock tool...you may want to be sure you have the latest. Although, I'm not entirely sure you still need to install the certificate anymore--I believe the new process did away with that step.
I havent done an Omnia, I did a Focus using the certificate method...but going that route didnt involve the ChevronLab unlocker at all. I restored all the way back to the beginning, unlocked, then upgraded each revjsjon one by one...
The Titan and Focus S that I unlocked within the last week were as simple as paying the $9, plugging in the phone and hitting the start button...
Head over to XDA...I bet you'll get some good info there for sure...
Good luck