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AdvantageDesign:
I assume EditCNC is a windows program. You did not indicate what operating system(s) this runs under, nor does their web site.
In any system that uses a new UART (meaning 16550 or equivalent --- these are not really that new) you should turn off the UART FIFO (internal first in first out buffer within the UART). This may not be a problem with Fadal, but it apparently is with at least some Fanuc machines.
I also have to assume that the PC where EditCNC is located is different from your DOS machine. If so, your RS232 driver may be different, lower voltage and/or current. Except you have now indicated you can load short files. But maybe noise errors occur on longer files. You have not explicity indicated whether the DNC errors occur before the Fadal buffer gets full. Until whatever Fadal's buffer is for DNC, and this gets full there will be no XOFFs sent. In part the question is whether the XON/XOFF function is working correctly with your computer.
If DOS works why change?
What is your cable length, have you tried a lower baud rate, and have you experimentated with simply sending a short file instead of DNC (drip feed) at different baud rates? Doing this multiple times to increase the probability of errors from noise.
Are you getting parity errors or something else? Does Fadal load data into memory and allow you to see the error. Knowing the nature of the error might help isolate the cause.
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