I can think of a few things.. First, had the break-a-way been pulled or shorted or other electrical fault I would hope the Prodigy would have told you about it.. But since I do not have one I can't be sure of that.
However it is also possible the brakes themselves may have a problem.. Was the trailer new or used (Used if it sat around they may have done strange things)
If the prodigy did not alarm, testing it is fairly simple, most RV dealers should be able to do it in ... Well takes longer to write the service order than to do the test.
If it's the trailer.. The dealer is where you need to be for that one too less you know how to do it.
And to end this post: If you happen to be near southern lower Michigan.. So is Tekonsha.