Our company builds board in millimetetrs, so I run in to this fairly often. I think, if I remember correctly, the default NC Parameters for Excellon Format is 2.5. In my case once a board get over 99.99999 millimeters in a direction, that format no longer works and I have to change to 3.5. I suspect this is your issue.
As for the NC Route, if you have slots defined in your board, NC Route will define those in a NC Route file similar to the drill file.