I will update this later, here is what we believe the RESOLUTION is:
1) User is using Ctr-P to print.
2) The problem is resolved by writing a script in Filemaker to print.
I will confirm this after I have gone over and made the adjustment and test to see if it does in fact resolve the issue.
When they use Ctl -P they are using the current print set up settings. I'd check them to see if B&W printing might have been specified in a prior print job for some reason.