It was exactly the same on my 996 almost from the first day I got it, I also found it was leaking slightly at the clutch slave cylinder so I replaced the seal and rubber bellows. Since doing that the fluid has remained clear for about 2 months now.
Replaced the clutch fluid last night, today after 70 miles it is once again black. Not really bothered it is not leaking anywhere and my Mille from 10 miles has been the same? Shoddy Italian sealing?
the only difference on the 996R is that pro twins have used a different hose to normal, they get it from Fords, not sure if this the result of clear fluid.