Thought I would give an update in case anyone else has the same problem.
I spent an hour in chat with support and they tried to help, but didn't come up with an immediate solution. I think it is being filed as a bug. Please let support know if you have any problem with transactions not showing in the app.
The transactions do show on the statements you can request through the app though, so they are in the system somewhere.
Now I am not sure if my balance is correct in the app because I don't know if the amount of the transaction has been correctly deducted or not.