That's really odd. There's a ton of cloning software like CarbonCopy, SuperDuper (i use this one) that can be used to boot a mac from an external drive despite it being from another computer.
I guess at this point, your option might be to plug in the mac pro disk into your mini and access files that way
Actually...
http://www.everymac.com/systems/appl...2.0-specs.html
If that is the one you have, that explains it. 2006 mac Pros are only supported till 10.7.5 and of course Mac minis dont run 10.7.5. But i'd go for a new GPU if you can find it. DL hardware while nice for basic reading and light internet, it's not so good for heavy duty work. Your mac mini will likely provide better performance over the 2006 under those conditions.