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.
"Susan smiled at me, giving Molly the Female Once-Overa process by which one woman creates a detailed profile of another woman based upon about a million subtle details of clothing, jewelry, makeup, and body type, and then decides how much of a social threat she might be. Men have a parallel process, but its binary: Does he have beer? If yes, will he share with me?"
-Jim Butcher, The Dresden Files