While debugging a model-based controller on a system, I came across the following situation:
I have two identical blocks, each defining a nonlinear, 2nd order continuous system model (it's a pendulum) xdot = f(x,u). The blocks output xdot, which is hooked to an integrator that is looped back around so that the next simulation step can get the updated state x in f(x,u). However, one block gets u = u1 from the controller output, and one gets it from a "Repeating Sequence Stair" block that contains the same command to the plant, u = u2, that the controller outputs (saved from a previous simulation). I've output the inputs to each block and shown definitively that u1 = u2, so as far as I can tell, the systems should be identical; they just get their inputs from different sources.
However, that's not true; instead, the solutions are completely different. I'm using a fixed time-step with a Runge-Kutta (ode4) solver. I've tried other solvers and it doesn't seem to affect the result. I'd really like to know how this is possible.
See this picture http://tinypic.com/r/33n9c0o/6 in lieu of the actual model. The plant input sources are in red, the blocks containing continuous model definitions are in blue, and the states/integrators corresponding to continuous model are in green (so the conflicting outputs are Position and Position1). There's a lot of other stuff but it's also all identical between the blocks and related to the discrete models anyway (i.e. not this issue). 
