[Mark McLeod]

Just at first glance...

In Periodic Tasks Your Encoder Example should not be within the 100ms loop, because it enforces it's own infinite loop it would prevent anything else you might put in that loop from ever running more than once.
Just drag it outside the loop and that's good enough.

In Encoder2.vi the infinite there needs to be throttled down. Right now it's sucking up all your CPU time running just as fast as it possibly can.
Just add a 100ms wait in there just like that used in the Periodic Tasks 100ms loop.

For DIO In.vi you don't have the correct input constant for DIO 9 or DIO 10.
See the tiny red dot where the wire connects?
Delete both of those and use Create->Constant to get the correct enum.