Thanks for all the thoughts and great Idea's,
Yes the battery disconnect was in the off position, I would think the Solar should still charge.
I don't know if the fact this trailer has electric over hydraulic disc brakes has anything to do with the low battery deal, but as soon has I have more battery power they work better and better I tried charging my batteries that day and the more power they got the more the brakes worked.
I still have no Idea why the solar didn't do its job, maybe to dirty? I don't think so. I have 2 deep cycle batteries it should have worked.
The truck has a built in brake controller I don't think the wiring would be bad.
I have pulled it before taking it back to the dealer a couple of times and the brakes worked to good at first had to really lower the setting on the controller, also after the weekend of charging once again worked like a charm.
Thanks for the comments on the setup we really like it also, I can't wait to take in on a real trip and see how it tows.
A few more days and I will see.