Two other things to consider trying...

How do you have your sub level adjusted? If you have the gain on the plate amp turned way up and your 990's sub trim down, you may want to turn the sub's amp down some and tweak the 990's trim (I've had a two-channel Parasound amp that didn't like being run with the gain controls all the way up, so I've tended to set my sub's amp at no more than half of its max).

How do you have your sub's crossover set up? If it's set to something less than the highest position of 180Hz (or simply bypassed, my preference), there may be something odd going on there with the sub's slope of the sub's crossover and the slope of the 990's crossover. It's quite a bit less likely than my first thought, but worth taking a look at...