Easyapache - disable enablefileprotect

Hello, At the end of EasyApache, "enablefileprotect" is run and it takes forever to complete. My file system is huge, with loads of inodes, so I believe this is the reason it takes a lot of time to complete. Even if I disable File Protection, it still runs and takes a long time to run, because it simply does the opposite. Is there any way I can disable this step completely, without having to change the script? By the way, this only seems to happen after a recent server migration. In my previous server, I am pretty sure this step didn't take so much time. Do you know what could be the cause for this process to take more time in the new server? I'm not sure if it helps, but the disk quotas is disabled, just like in the previous server. Thank you, Nuno