It does sound like the media could be too tightly packed, that instead of an aerobic environment, where normal beneficial bacteria thrive, that an anoxic environment has been created.
Cramming more and more media in a small space does not mean you get better bio filtration.
The population of beneficial bacteria is not determined by amount of media (as long as it sufficient), but will be limited by metabolism output of the fish in the tank, and aerobic condition created by flow.
If it were me, I'd remove some a little at a time (maybe a handful or two), and test the next day, to determine what is the a sufficient amount for the tank.
It may turn out half is "better" than a large amount
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The chamber holding the bio-media in the sump above is only about 1 ft square, lots of interstitial space between chunks to allow unimpeded flow, and is sufficient for my 180 gal holding 15 fish mostly @ 5" in size.
The flow thru the sump creates this type flow and surface agitation in the tank.
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The outflow of each pipe is 1", except the 2nd from the right 1/2", because of water lilies in its wake.
I also use lava rock, but I leave it in 1" to 2" chunks.

as you can see the flow allows for enough space to create aerobic conditions