Yes, you can have all sorts of funny problems if the file does not end properly. This is even mentioned in the Mach3Mill manual somewhere (section 10.5). At the least, it MUST have a <carriage return> at the end of the last line.
As Craig suggested: put a '%' at the end of the code on its own line every time. (I think that too is in the manual - somewhere.)
Cheers
Roger