X's 2 on working with John, a knowledge base!
A few thoughts:
> Does the control board in the Aqua/Hydro Hot bay reflect any error codes?
> Have you checked your fuses?
> Once the Aqua/Hydro Hot fires up and say two or three minutes has gone by for the temps to get up, reach in and touch the pump to see if it is running.
(The heated fluid needs to be pumped to the different heat register areas. If the pump is not pumping, the hot fluids are not flowing to the registers.)
Combo's of the above are worth checking too...
I also follow the advise of a few veteran Aqua/Hydro Hot heat owners, where I regular 'exercise' the full system. Fire things up on diesel, turn on the heat, and keep the fluids flowing to the registers. And the sub register pumps, depending upon unit. Same as running the generator and the AC units, etc., etc.
Best of luck to you as you sort this out, and please, circle back and close the loop once you determine the problem