I've taken a quick look at your Mach4 profile and I don't see anything that should prevent the spindle PWM from working on pin 16. I did see that you have the charge pump set to "on always", which is not a usual setting except when connected to a Geckodrive G540. But this *should* have no effect on the spindle PWM.
When you looked at the PWM signals with your 'scope and saw it working on pin 14 but not 16, were you looking at I/O the screw terminals on the Xylotex board? And was the Digispeed wired to pin 16 at the time (and not wired to pin 14)?
If you haven't already, try testing with just the PMDX-411 and the Xylotex board, with the Digispeed not wired to the Xylotex board. Then see if you get any output on pin 16. If you get PWM here but not with the Digispeed connected, then the Digispeed may be loading down the PWM output signal.
As two last resorts, unplug the PMDX-411 from the Xylotex board and see if you can look at pin 16 directly on the PMDX-411's DB25 connector (you can ground the scope to a good ground on the PC). If you see the PWM on pin 16 here but not when connected to the Xylotex, it is possible that the ribbon cable is faulty, or that there may be a faulty trace on the Xylotex board (not likely as you said this worked with Mach3 and a standard parallel port.
Bob