I have 2 green LED lights on my dual pro charger but the batteries do not seem to be charging.  Left plugged in all night and still not taking a charge.

If they're standard flooded batteries, take them to the local auto-parts store and have them test the batteries...most do it for free. Could be bad plates.

 

AGM - if you discharged below 10.5v, the charger won't try to charge them. Take them to the shop, they have the knowledge/equipment to regenerate a 'dead' AGM.

Your onboard shows charged with the green LED.

Something is haywire. 

Harbor Freight sells a Chicago 12V battery tester under load with voltage meter well worth it.

Assume you know what to look for like low fluid level for wet cell battery, corroded terminals etc.

Tom

Two green lights?  Flashing or on solid?  Why do you think they are not charging?