My guess is it would have to do when his best/worst seasons with respect to RA-9/FIP came from relative to league average?
For instance in 98-99, at the height of the steroid era, he had a 3.25 ERA in '98 and a 3.54 ERA in '99, with FIPs of 2.77 and 4.07 respectively. That averages out to a 3.42 FIP for those two seasons, and a 3.40 ERA (presumedly slightly higher RA), yet the RA9-WAR is 12.3 and the fWAR is 11.6.
You have enough of those tiny differences between enough seasons and since WAR isn't exact to the decimal place, you end up with a career fWAR of 79.8 and 81.0 RA9-WAR.
Edit: for further reference, league average ERA/FIP was 4.43 in 1998 and 4.71 in 1999.