According to the Jean Acheson declaration (BK#167):
6. Since that time, the Debtors have repaid Novell all of the undisputed royalties on a timely basis, but Novell has failed to ever repay the Debtors the 5% administrative fees due to the Debtors under section 4.16( a) of the APA.
That sounds like SCO is claiming that the 5% was never paid. OTOH, if Novell had been failing to pay the 5%, it's unlikely that SCO would have waited until now to bring it up, especially while Novell was arguing that SCO breached their fiduciary duties in front of Kimball.