Since you have the PMDX-424's "COM" connected to the "PUL+" and "DIR+", there are a couple of configuration things you need to pay attention to:
(1) Tell the PMDX-424 to output +5V on it's "COM" terminals:
Go to the "Configure" menu and select "Plugins...". Click on the "configure" button for the PMDXSmartBOB. In our configuration dialog, click on the "Motor Config" tab. In the top right look for "Step/Dir Common Configuration" and select the "+5V" option.
(2) Set the step pulse polarity. When the COM is +5V, the step polarity needs to be "active low". Still in the PMDXSmartBOB plug-in configuration dialog on the "Motor Config" tab, change all the "STEP Polarity" settings to "Active Low".
(3) Direction polarity: this you will have to experiment with to get the motors to move in the correct directions. The polarity setting depends on how you have the motors wired to the drivers.
Bob