That's very odd Sam... most confusing.
At this stage the options I can see are:
1. Give it a bit longer, maybe try with your original media that's in my filter.
2. Complete water change to remove ammonia, then buy the betta and test daily and change water as necessary - ie, do a fish in cycle (which may even not occur with mature media).
3. Put your original media back in in case that's the issue and then fish-in cycle.
What do you think to doing that?