Mike - I have this problem when using my download version to run some copper clad etching programs which often go to several thousand lines. When I download them, they only load to the 500th line - you can see that in the download window. Another dead giveaway is that the toolpath diagram does not show the whole cut, (only the first 500 lines).
If you say you have purchased a copy of Mach 3 this should now open up to do the complete number of lines.
You can, if you wish, test this by cutting 450 line chunks out of the program using notepad and adding M99 at the end.
If you just do a couple say, using "save as" name them p1 and p2 and file then in the "subroutines" folder. In your main program, where you cut them out, type in M98(p1.txt) and M98(p2.txt) and load that.
You should find that your Toolpath display now displays about 1400 lines of the code - two 450 line subroutines and the 480 or so lines after that. I am not suggesting that you do all the program like that, it would be far to taxing, put it will point to where the problem is.