Hi Amied, the problem is from using a cracked V3 old beta version. That function for automatic booleans with face extrudes is in the final v3 release, not in that old beta release.

If you purchased MoI you can get a download of the final version by putting in your license key here:
http://moi3d.com/beta.htm .

If you're using a cracked version please do not ask for support for it here on the official forum.

Thanks, - Michael