Does your thinner, harsher bottled beer have higher carbonation? One way to rule out or narrow down a possible infection would be to pour a bottled beer into a sanitized glass or hydrometer test jar. Stir it for a bit to get the co2 out of suspension then take a gravity reading. If the gravity reading is significantly lower than it was at bottling, you may have infected beer.
I would then start looking at all of your sanitation on the bottling side of things. I once lost 3 consecutive batches to a gusher infection before I noticed a tiny cut in on of my transfer hoses.