Daedelus,
Last evening, I set up Eagle V6.x so I could see how your program would work. Everything seemed to go fine, but I would like to offer a suggestion.
I can speak only for myself, but for PCB use, I have a fixed fixture on my machine and for doing operations on the TOP of the board, I use fixture 54. For Operations on the bottom of the board, I use fixture 55. So when setting up, I home the machine and load a previously saved fixture file that automatically gives the proper offsets to the various fixtures. Of course as setup, your program does not include any fixture offsets and I would suggest adding a dialogue box to indicate which fixture is going to be used when you parse an individual file. I say give the option to set one because as you say, this can be used for other operations other than PCB work and who knows what fixture offset may be needed?
Thanks in advance and so far, really like how things are setup.