Just a guess, but I'm thinking the 90 minutes is in fact the boot process. I've seen, and there are plenty of posts on the forum about the time taken to re-acl all the samba shares.
On our server this took around 20 minutes to boot up (3.0 at the time), and the later versions of Zentyal seem to boot faster, but in fact get to login quicker but haven't started all the services, so the web interface isn't really present.
It's easy to see, just run a shell or ssh in and look run top and you should see the boot process is still happening.