The api test kit picks up total ammonia. That is it shows ammonia Nh3 and ammonium NH4. Ammonium NH4 is non toxic to your fish. That is what is most likely going on.
if you want to test for ammonia only I would suggest a test kit like one from seachem which can detect for NH3 only.
To have high levels of ammonium usually means your water conditioner has converted the toxic ammonia into ammonium which your the bb bacteria feed on.
It appears in your situation that your bb are not working properly because your bio media has recently been disturbed through cleaning / not enough not efficient / become clogged. Never rely on gravel as a bio media !
I would replace 1/2 the media on your setup and fill all the trays of your c360 with high efficiency bio media with some mechanical filtration in the top tray to keep the bio media from getting clogged, leave the magnum to do the main mechanical cleaning with the pleated micron filter.
Essentially I would treat the tank as having a mini cycle and prepare the tank by adding bb products such as seachem stability until your water parameters are back on track. After X period of time when everything has settled then I would replace the other half of the old media.