I wasn't able to look at what your file looks like, but for some milling files the machine's acceleration times can make significant differences in what the actual milling time is, especially on machines with low accelerations and high feed rates. The machining time estimate in Linuxcnc does not make any allowance for machine accelerations, and none of the run time estimators in cam programs I've used do either, other than sometimes adding a time percentage to the estimate as a fudge factor. The result is files that have lots of changes in direction with short moves can have the actual milling times be wildly different from their estimated time. (I have never tried Fusion360.)
Be sure that the feeds specified in your files are within the capabilities of your machine and the feed rate limits you programed into your ini file.
