[FRCMikeH]

Problem solved.

We implemented a state machine that checked the tick count vi to check the elapsed time. If the time expired we went to the next state otherwise we stayed in the current state.

Greg, we tried your advice, but it didn't work. In theory it should have so it could have been our implementation, but I think it was good. We did the following:
Put our slow retract piston in a while loop at the top level of robot main. Then we enabled the code using a global variable from the teleop vi. Unfortunately we saw the same problems.

Anyway, problem solved. Thanks for your help!

As a side note, we built a subvi wrapper for the 'wait' vi to feed the watchdog time because our wait statements were causing watchdog timer errors. Have others had to do this?