I set up a simple back and forth shuttle route using my CS3 and S88. I got the event to work but when I went to use it again after several days I have some issues. First off when I start the event it starts it at the midpoint of the event and takes thebtrain to the second stop/station where it stops as it should. The train starts again but the event stops and thus the train goes toeard the first stop but the train does not stop at the first station as it should. Any ideas on why this is occurring and how to fix.

Events in the CS3 are not nearly as simple as with a CS2. I would delete your current shuttle and start again. If you have the Marklin book try to follow the instructions step by step and see how that works. It is easy to make a mistake when setting up events and does no harm to have another go at it.