Yes, avoid Thrifty at SJC
Rented from them early last year. Not quite a horror story like yours, but I will definitely remember it for a long time. Fortunately, I used AmEx, which takes a rather robust attitude towards unethical merchants.
Ever since I switched to Hertz, where I am now top-tier frequent renter. Their customer service is utterly amazing, and I will gladly pay $10-20 per day more to rent from them rather than from morons like Thrifty.