I think you may be experiencing the same problem I am. I was doing batch imports OK with earlier versions of FCP, but ran into a problem the first time I did it in FCP HD.
My batch import text file showed the timecode numbers with a semi-colon before the frames indicating the correct drop frame mode. But after I imported the text file, the shots showed up in the FCP browser bin with all colons, and the numbers had been converted to their non-drop frame counter parts.
Was your original material drop frame? If so, the TC numbers should have one semi-colon before the frames, or all semi-colons. If this is the case, what about the shots in your bin after you imported them? If you have the same problem I have, all your imported shots will now show all colons.
If you have a TC converter program, type in one of your original numbers as drop frame. Then convert it to non-drop. Does the new number match the seemingly "random" number in your bin?
I really think this is a bug, and I'm interested in knowing if this is the same thing you have. If so, I did figure out a workaround. Let me know, and I can send it to you.