Large Registry after C2

While applying the C2 standards to our NT4 IIS server and during the registry phase the registry expanded to over 32MB and an error was generated. So we expanded the registry allowance to 80MB and rebooted and re-applied C2. The same happened, except this time we expanded the allowance to 128MB, did not reboot, ran the C2 program. The registry eventually settled at 82MB, 2MB larger than the 80MB restriction we had on.
Regclean only did it’s usuall and removed redundant entries, but had not effect on the size (to be expected).
What now?