SEPM 12.1 MP6 RU5 - Setting ACL

I'm currently upgrading SEPM 12.1.6 MP5 from 12.1 RU6 MP3. Everything was going fine, but I've been stuck on "Setting ACL" for nearly an hour and a half. The SetACL.exe process is running and using CPU, so I don't want to kill it.

I have run a DB backup, and stopped the SEPM service on this server prior to the upgrade.

I was wondering if anyone else had to wait a really long time for this step.

Thanks!