Oops - Steve answered as I was typing this. Lets see if I can offer anything in addition to his answer.
The short answer is that if it works properly for M3 and M4 commands, then it is OK. Just know that the spindle will run backwards when using the PMDX-107 test mode (which you should only need to do when setting up your machine).
If you want the PMDX-107 test mode and your M3 commands to both run the spindle in the same direction, then keep reading...
The PMDX-107 has several LEDs on it, including one for each of the solid-state relay outputs (in your case, one for "Run" and one for "Dir"). These are located just below the screw terminals for these two signals. When you use the PMDX-107's test mode, the "Run" LED should light up and the "Dir" LED should remain off.
When you issue an "M3" command, does the "Dir" LED on the PMDX-107 light up or does it remain off? How about an "M4" command? I'm betting that the "M3" command causes the "Dir" LED to light up.
Since you are using a SmoothStepper (well, you were in your previous posts), you may need to tell Mach that the spindle "direction" signal in "active low". See our app note AN002 on page 5 of the PDF document (
http://www.pmdx.com/AppNotes). If you are running Mach4 then I'm not sure how to configure the spindle.
**HOWEVER** making the M3 command match the PMDX-107's test mode will run your spindle backwards. So you should also check your VFD manual to see if there is a setting that controls how its "Direction" input works, if there is such a setting. Or reverse the wiring as Steve suggested. If you cannot change how your VFD interprets its direction input, then leave the the current Mach/Smoothstepper settings alone and just remember that the PMDX-107's test mode will run your spindle backwards.
Bob