From what you've written, can we interpret that the chassis batteries hold a charge when directly hooked to a separate trickle charger but when on shore power for a few days, the chassis batteries are dead? I don't know how long you're leaving it on shore power but could the parasitic draw be draining them to a point where there's not enough juice to start? If so, maybe install a Trik-L-Start? ...or keep the trickle charger you have hooked up too when on shore power?
I don't own a Thor but from what I've read in the past, they don't charge the chassis batteries on shore power. That's why I've talked to several Thor owners who have installed an ISL Trik-L-Start (or Amp-L-Start).
The ISL product seems to be the most popular but you could also use a similar products such as a Xantrex Echo-charge, etc.
But again, I'm not sure how your coach is set up or if I'm even interpreting your explanation correctly.