[DavidGitz]

Here are some "issues", although none of these I don't think are the cause of your problem:
-You should not need shift registers. It is still passing the same reference.
-The +1 in your while loops isn't needed, i is incremented automatically. (unless you want your while loop to run 1 less than the indicated number.
-I would reduce the timer value to less than 50 mS, like 40 or 20. There isn't really any reason to run it longer.
-We like using the express vi "Elapsed Time" instead of looking at the the i value. It is easier to program and I think it's more consistent.

But I think your issue is either in your references (check the Begin and make sure they match) and check if it works in Teleop. If it works in Teleop it is a Programming issue, if not then Electrical.