I took the rear derailleur off my bike, and replaced it with an ultegra 9-speed long cage derailleur. I have a 12-25 8 speed cassette in the back, and 53/39 in the front. I used the same chain that I was using with the old derailleur (a short cage dura ace 9-speed) - the length appears to still be correct. It will shift into all of the gears, but it clicks a lot in the gears on the big ring.
From what I can tell, it looks like the chain doesn't sit quite flat on the outer derailleur pully - its a bit off to the side. Adjusting the limit screws doesn't seem to help this. The derailleur cage doesn't seem to be bent.
Does anyone have ideas on what could be causing the derailleur to act like this - is it the long cage with a double, or could something be worn out (I got the derailleur used at a LBS - not sure about its history)?