I believe the JP3 jumper is shipped in the off position. Just to be clear, you are powering the ESS from an external 5V power source and not through the PMDX-126. If this is the case, then this jumper should be fine in the default setting. Are you getting power to your ESS? Otherwise, what led you to question the JP3 jumper?
When you started to install the new PMDX-126, did you follow the Quick Start Guide in the PMDX-126 manual to test and verify your PMDX-126 was functioning correctly before proceeding with the install? It is best to verify it is functioning correctly and then slowly add new connections, retesting after making the new connections. Having everything connected before testing makes it very difficult to isolate issues.
Your description of your issue is quite vague, and additional details would make it easier to guide your troubleshooting efforts. Are you sure the issue is with the PMDX-126 and not with any other component?
If the "E-Stop" light is on (bright red light), then the "Output Enabled" light will not come on. Do you have an E-Stop button installed with a normally closed switch connecting the E-Stop pin (pin 4 on J13) and the GND (pin 5 on J13) together or is there a jumper installed between these two pins? The PMDX-126 is shipped with a jumper installed between these to terminals and the PMDX-126 is designed to only function when these two pins are connected together. Are there any other faults, perhaps from external components such as motor drivers, that are causing pin 6 (Faults, active low) to activate. The PMDX-126 will also disable outputs if faults are present (or it thinks there are faults present).
A couple quick tests you can perform to determine if the "Outputs Enabled" is in fact on (e.g., the "Outputs Enabled" led is not functional, but the rest of the board is):
1. Connect an 5V LED between J7 pin 2 ("OE") and pin 6 ("PCgnd). The LED should light if the outputs are enabled.
2. Configure the K2 relay to be enabled when outputs are enabled. JP2 connected between pin 2-3 "multimode" and set dip switch "Config 8" to open (off), then press the "Test" button or perform a power cycle. Connect a LED or something else (contactor, etc...) to the K2 terminals and if the outputs are enabled, the device connected should activate if it is connected to the NO terminal or will deactivate if connected to the NC terminal when the outputs are enabled.
Without more information, I can't think of anything else to verify the PMDX-126. If you are still having issues after following the suggestions presented, then follow-up with additional information. Best of luck!