I am the Plugin author. The Plugin works by filtering the output of the current post, comment etc. and does this regardless of the posts published date.
I have not heard behaviour like this before and I am sure I would have by now if you could only filter NEW posts after the Plugin was activated. It would be a pretty useless Plugin in that case.
Sounds like it could be a Plugin conflict somewhere. If possible, test the Plugin on a clean WordPress install (preferably with the official sample data) and you will see that it works fine. Try deactivating your Plugins apart from this one and go from there, reactivating them one by one until you find the problem. Perhaps another Plugin is also filtering content that is conflicting with the way WP Content Filter works.
Hard to say from the information given.