I've got a 406A. Heater was non-op when we moved in, and didn't have heat during our first season. Loads of mice had moved in, and ate the majority of the circuit board.
Anyway, once that was all ironed out and it fired up, I had the same issue. Not a lot of heat, had a kind of a lazy blue flame, etc. If you need tech help, call Raypak themselves. They are awesome (Another pack of mice moved in, ate the digital readout, and they sent me a free one).
They had me take the front off, and really blast it good with air. Get all the junk out. After I had the innards near spotless, there was really good, really fast, heat.
They seemed to think that a buildup of 'junk' had an effect on the potency of the heat. Yes, heat is heat, but what you want is a true-blue flame. After I was done, I went from lazy blue to a strong blue. No dancing yellow.