We noticed this slowness even before the site was made live so there would only be two people even hitting the site at all. Then it was REALLY bad, especially when loading the first page, but we found that hiding unused courses made it at least workable.
Interesting post - let's focus on your PIX problems first .
I'm wondering what in your PIX config causes this failure of uploads. We have the moodle server running behind two PIXes without any issues at all. Can you possibly post back what that HTTP traffic setting is (if there is a security issue - then email me)? If you can get back to using http for normal work, then it may reduce the load on your server quite a lot and make the site more responsive for your users.
We had a similar problem with SMTP inspection on the pix munging up connections to the exchange server in a similar fashion. IT was a known issue and the only fix was to shut off the smtp inspection entirely.
You're right about that inspect http command. From what I've read, there's a performance hit on the PIX and the overall suggestion is to turn it off and try reverting back to the fixup protocol http 80 command (which is what we have in our configs). There's due to be a patch from Cisco out for this in April, so wait until then. We're still on version 6.x of the PIX IOS, which explains why we're not experiencing any issues.
You're also right about the lack of specific Microsoft SQL Server notes in the performance docs. But that is probably because support for it is new - give it time and I'm sure more will be added .