Just make sure you hold the bike level and not on the sidestand when checking the oil

I also filled 2.9L This problem is also treated in this thread http://www.xt660.com/showthread.php?t=16450
I took out some oil without unscrew the drain bolts.
I used a water plastic bottle 0.5L with large cap.
On the cap of the bottle i drilled 2 holes. Though each hole i passed a transparent plastic tube ( 8mm) into the bottle. One of the two outside ends was placed in the oil filler hole and the other the other one was used to suck air out.
I took out aprox 300 ml considering the 0.5 L bottle used. I couldn’t find a syringe.
I ride it 60 km and than checked the oil level: bike straight up, waited 3 minutes (had to wait was leaking) , the cleaned dipstick inserted without screwing it, and the level seems to be at the max.
http://img819.imageshack.us/img819/9204/levelg.jpg
This oil level check seems like rocket science.

I've changed the oil on mine 3 times,every time 2.6L doesn't even show on the stick,to get it 3/4 of the way up the stick need another half liter any others have this problem.

Done a few oil changes and when i had my bike in getting the valve checked got the my local mechanic to also change the oil. He said he put in 2.6ltrs of oil, but i never trust people so started the bike took it for a short spin around the block, checked the level of oil on the dip stick and no thing, half a litre later and we where sorted. Took a long ride home and checked when i got home and still the same about 3/4 up the dip stick.

Never had this problem at home as i never new how much i was putting in, was always a rough guess!!!!

The engine is not over full... The tank is over full
the engine will always have to correct amount of oil in it..

I see checking the spec of the latest XT's the oil quantity is 2.9L

Well the experts have always told me that better 100mL BELOW the MAX level than 100mL above, as excess oil leads to excess oil pressure and that can cause all sorts of engine damage, so always better to stay just below the MAX mark......

This is basically true imo. But if the frame tank is overfull, I think oil will drain out of it back into the engine, thus causing (in extreme cases) an overfull crankcase with its attendant problems. I doubt that 300ml is much of an issue, but I imagine one shouldn't check the oil...

Not a case of over filling, unless I put 2.9L in it won't even show on the dip stick.

It's strange that basically the same engine/frame configurations can vary so much. Mine will only take 2.6L to be at the full mark, but there you go. I'd be happy if it did take 2.9L. More oil is good.