Well, a lot of folks don't want to be bragging on their radios.
I have owned the 990 for around 6 months and rate it a 5/5. If you are interested in my evaluation of the 990, read my eHam review. And if you'd like additional reviews, there are 40+ reviews on eHam.
The fact that you see a few for sale does not necessarily suggest anything negative about the radio. There are lots of other possible reasons for sale.
I just got off of the phone with a friend/ham that I have not talked to in at least 9 months and during the middle of the discussion he casually mentioned that he had bought a Kenwood 990. I paused for a second and said What!! You got a 990 that's fantastic, you must be in heaven! He replied yeah it's ok, it's not bad, etc etc. (in a dull unexcited tone). I asked him if there was something wrong with it and he said no it's ok.
I have talked to two other 990 owners on the air and they also sounded a bit reserved about the radio, not something you expect from Hams but hey I thought maybe these guys just wanted to be modest. The thing is I really prodded my friend on the phone and the only one who sounded excited about the 990 was me.
So what's up with this great looking nice sounding radio, why are so many owners so silent about this lovely looking piece of gear, is there a problem, is it unintuitive in nature, a pain to use, what? I also have seen one on eBay and one on QTH for sale at about $1000+ less than the listed price.