I had several 03 and 04 KX250s that acted the same as yours and all of them turned out to be a crank seal. At first we tryed to rejet without any improvement. I went through several race seasons trying to find the issue. Spoke to factory reps and changed 2stoke oils brands. It ended up being an ethanol problem. Some may not believe that that was the problem but I switched to straight 110 Cam 2 race fuel and all my crank seal problems ended. Ive been using it for over 2 years now without any seal failures. At first we were using 1 gallon of race to 4 pump and I was replacing seals twice a year on 2 bikes. We switched to a 50/50 mix and our seals lasted almost the whole season. We finally switched to 100% race and the seals are still in there after over 2 seasons.
Symptoms with our bikes.
Bogging/breaking up at high RPMs Smoking like crazy!
Thick black oil dripping out of the silencer
High trans oil consumption at the faster races, higher rpms. Didnt notice it as much at the tighter, more technical races where the rpms are low.
The clutch side seal would come out rock hard everytime.
Try rejetting, if that doesnt help I would look toward the crank seal. The bike is 9 years old. Unfortunately you have to split the cases to replace them. Cometic sells a viton rubber crank seal set that resists the effects of the ethanol allowing you to run the crappy pump fuel.