As much as I hate to admit it I feel the same way. There is such a difference between the 2 volumes that it's almost like they were letters from 2 different people.
I've only read Vol. 1 of the letters, but I've also made the observation that the Burroughs who produced Junky
and Naked Lunch
inhabited a completely different psychological and social universe than the Burroughs who gave us the cut-ups, and particularly the works that followed, e.g. The Wild Boys
and the Red Night trilogy. I'm sure this frameshift is reflected in Vol. 2 of the letters.
A lot of it has to do with the overwhelming intellectual and social influence of Gysin. Burroughs clearly saw Gysin as his intellectual superior and wound up repeating all of his mantras. Some of the influence was positive, leading Burroughs' work into new directions with he cut-ups (some of the end results were interesting, others less so), but Gysin also filled his head with a lot of nonsense. And Burroughs' early attraction to the ridiculous Scientology cult (the "intellectual" contents of which, e.g. thetans and engrams, are clearly designed to attract people at the far lower end of the Bell curve) still boggles my mind.