[Mark McLeod]

Much better to look at.
Unfortunately, I don't see anything wrong with how you're handling the timers in Autonomous Independent.vi unless it's a problem in "auto kick and solenoid logic.vi" which I don't have.

Running through that selection logic every time, even after the initial selection due to DIO has been made, may not be working right and could be the cause of the problem. It'd be easier to trace the logic if that vi was posted too.

It seems like you should just be able to just test for the rising edge of the Ball sensor DIO to trigger everything.
a la the attached. Note I increased the rest timer on you too.