Agree with Uriel. Most of us just run ceramics, sponges and polyfloss or some combo of those and hardly ever replace any media unless it's damaged, unless we work in a small amount of fresh after a long time.
It sounds like you have good weekly gravel-clean-water-change maintenance but that that is not matched perhaps by your filter maintenance. A U2 in a 90L might need to be cleaned more often (funny, kind of opposites, less replacing, more cleaning) than two months. Instead, try increasing that to monthly, squeezing out the sponges in the just-removed tank water (as I'm sure you do now.) The bacteria are like a brown stain on media like a sponge and if you have a mature filter you will not necessarily lose too much bacteria by letting more debris get cleaned out rather than less (it's a little hard to describe.. you don't want to wring sponges out so much that it's too much but on the other hand you don't want to be so timid that you don't get the bulk of the organic debris out.
Any excess debris filled water in the filter needs to go out too and the box interior itself should get cleaned. Perhaps there is some way that a fair amount of organic debris is managing to stay within your sytstem past cleaning episodes.
If, after another year or more I suppose, you are still having problems, you might want to consider a significantly larger external cannister filter for the tank. Many of the smaller EC units are sized quite well for a 90L I believe.
~~waterdrop~~
