Duplicate Data almost always occurs because you either have Pocket Informant reading from two data sources that themselves look at the same source, or because of working with sync accounts you didn't delete the data associated with it.
Check to see if you have iOS calendars on. If you use both sync and iOS calendars with the same data, you will see duplicates. Pick one or the other.
If you remove the Pocket Informant Online sync account without removing the data associated with it in, and then add it back and resync up, you will upload all your local data to the server again.