Autonomous not stopping. Constantly running... during enabling

[RufflesRidge]

Either of the two posts above should put you down the path of solving the issue.

The code you have now (in addition to not actually stopping the motors in the else) is creating a new timer every time autonomousPeriodic is called. This timer is never started so it will return 0. You can either create the timer once as 'heuristics' has suggested or scrap this and use a command with setTimout() and isTimedOut() as 'euhlmann' has suggested.