I think you're all right Linnea, Veronica, and Steve. Doing PT stretches and exercises designed specifically to strengthen muscles, tendons and joints to eliminate RSI or TMS symptoms does reinforce your programmed pain patterns. However, TMS programming is much more insidious and ingrained than just a series of stretches or exercises. The TMS mind is conditioned in all sorts of sneaky ways apart from conventional PT. For example, pain can occur when you walk uphill (but not downhill) or vice versa. When you run it hurts, but when you ride a bike it gets better. Or, in another case, you walk upstairs and feel weakness in your left leg, but walking downstairs is fine (on some days, but not others). These weird pain symptom discontinuities are pervasive throughout all the mental and physical activities of a person with TMS. You feel a tiny itch under your arm one day, you focus on it, and sure enough the next day it itches more and more until after a week of growing discomfort you are obsessed with it enough for it to successfully distract you from your underlying repressed emotional issues, whatever they may be: rage, sorrow, anxiety, fear etc. etc. etc.. But yes, eliminating PT from your schedule does go a long way toward short-circuiting the programming you've acquired from the medical-therapy establishment.
To throw my two-bits in, however, I've found that Pilates exercises do function as a kind of mindful meditation that tends to short circuit the TMS process. I think it's because Pilates exercises on the cadillac and the reformer machines require that you simultaneously focus your mental attention on self-consciously holding your core muscles in place, breathing, and performing choreographed motions with your muscles. What I think this does is shift your center of attention from your unconscious mind to your rational neocortex, thereby, in effect, changing your brain chemistry in such a way that TMS no longer sends impulses through your nerve pathways. But in this sense Pilates is functioning as another kind of mindful meditation like Pranayama breathing exercises that force your attention self-consciously onto your willed rather than autonomic breath. Remember that breathing is both voluntary and automatic and thus serves as an intermediary between both areas of the brain. But aside from this personal hobby horse, I think you guys are absolutely right to abandon all those absurd back stretches! I think what you should ask yourself is, "Have they ever done me any good? Have they relieved my TMS pain?" Invariably, when I asked myself those two questions, the honest answer I received back was, "No way!" They may keep you occupied while you move away from a particularly traumatic episode or period in your life that initiated the TMS pain response, but other than keeping you busy and occupied, they've never seemed to do a frigging thing for me!
But I don't worry about it, I assume it will pass as my various muscles get stronger. My trainer emphasizes core, breathing, and balance. She pushes me way harder than I would ever do on my own, and I've really started seeing a difference in muscle tone - it's really cool. Esp. at my age! I also take a serious walk at least twice a week and I attend a weekly aerobics class. 
