Not sure that Mazak understood your problem completely...
If I had to guess (don't do too much with lathes)... Interference checks are having an issue with collision. If you're really that far away from the anything, then perhaps your parameters need adjusting for the interference areas. It might be set for max or extreme coniditions (oversized chuck, short chucks, etc). Are you using Mazatrol or EIA? I will assume Mazatrol won't work because it initializes collision checks right away.
You should be able to set your tool length off manually without using the Tool Eye and Tool Data should accept it. Then in EIA, I would expect if you shut off the interference check buttons and perhaps turn on Barrier Cancel, it should run.
Throwing rocks at a wall here....