I also have exercise intolerance which I experience as stiffness (the tin man feeling), rubbery legs, and a slight loss of coordination when running on the treadmill. I definitely associate it with BFS vs. getting older or being out of shape, since I've been exercising regularly for several years now and the intolerance happened right around the same time as my twitching started.
I've had to reset my expectations a bit -- if I can only run for 20 or 30 minutes vs. 40, or have to go at a lower speed, that's OK. Actually, having to stop sooner is kind of helpful since I go to the gym before work, so stopping sooner helps me get to work on time! (There's always a silver lining...) Also, I've started using some of the other machines more like the elliptical machines, which are a little less fatiguing and get some of the other muscles involved. And I haven't noticed any difference at all using the weight machines, which is nice.
I am finding after a couple of months that my running stamina has improved a tad, so perhaps I'll continue to regain my endurance. Hopefully the same will happen for you as well!