Can you discribe the odor? And are you certain that the odor is coming from the paint? How did you strip the paper? Did you use water? Could some of the water have gotten into the flooring and have sparked a fungus growth(Unlikely but possible)?
On several occasions, I've had to give up trying to clean off the paste and just go over it with a primer. Aside from the obvious problems of a latex going over a water soluable paste, I've never smelled anything strange. Chemical reaction? Sounds like BS to me. Don't take my word for this, but the only thing I can think of is materials that have past their prime (no pun intended!) Latex materials can go bad and the odor they give off is almost like a sewage smell. It's hard to imagine material at a Sherwin-Williams going bad, especially something like Pro-Blocker. They just sell too much of the stuff for it to sit on the shelf long enough (in a closed can, it can take years for latex to go bad).
If your problem is indeed coming from the paint job, I would recomend going to a Benjamin Moore dealer and getting your materials there. Especially if you can find a little "Mom and Pop" store. You'll pay more there, but these people usually have expirence in the painting trade, and have actually swung brushes for a living. The best product for blocking an odor like this would be BIN primer. However, BIN is incredibly difficult to use, so the next best would be something like KILS or CoverStain. These are solvent based products and will require ventilation while you use them.