Double check the cables on the three house batteries to be sure all are on the proper terminal. Maybe you can find a diagram showing the cabling. Is it possible you left a ground cable off of the house batteries, or may be a red positive cable?
Your house batteries should be wired in parallel and the cables should look like the cables on the 12V batteries in the image at the bottom of this reply.
The chassis battery problem is highly unlikely to be related to the house 12V problem you are now having.
If you don't have a volt meter, now is the time go to to Walmart--Home Depot or other place and for under $20 buy on.
With the meter you can start checking voltages at the batteries, the output of the inverter/charger, etc.
The fact the Freedom panel shows 13V indicates it thinks it is sending power out, but probably it is not getting to the batteries and other 12V systems.