Ok, if your hosting platform is Ok this seems to put the prob back to your site.
Presumably your old site i.e pre-upgrade to 0.9.6.2 didn’t exhibit this behavior, in which case its beginning to sound like something in the upgrade maybe.
I still think you should tell the site admins about the forbidden access to /home error, it shouldn’t really do this whether its pertinent to the fault or not.
You could try putting the timing marks out on a test page, i.e this syntax from the MODx template :-
MySQL: [^qt^], [^q^] request(s), PHP: [^p^], total: [^t^], document retrieved
from [^s^]
This will tell you roughly where the time is being spent, MYSQL or page serving. Bring this page up when the fault occurs.
Other than that you’ve only really got the logs to help you at the mo.
By the way whats an ’rc2’ that you mention above?