Web settings Foobar'ed upon upgrade to 10.4.9

Last night we upgraded our Dual G5 PowerPC Xserve with the latest 10.4.9 update (we were running 10.4.8) and it has caused several problems.
First off, we started getting calls early this monring that some strange page was being displayed if you tried to visit our main site. This was some kind of new default index.html "server is here and running" page.
This overwrote our existing "index.html" home page for our company. Here's a copy of that page that the Apple server software update placed into my Documents path (see http://www.classjuggler.com/index.html.server).
Something like this should never happen during an OS update for critical services such as Web hosting. If Apple just wanted to provide a fancier "here I am" page, it should have gone in as "index.html.BAK" or something similar.
Secondly, after restarting the Web server our SSL passphrase was no longer recognized? I am not sure if this is standard policy, but I cannot remember having to ever re-enter this before after any OS upgrades. And tracking this information down wasted us another hour of downtime.
As far as I can tell there was no mention of these two, in my opinion critical, issues in the release notes for the upgrade which has made this all the more frustrating.
Has anyone else run into these problems?

Why this happened is an unknown, and certainly a basis for a valid complaint, but no vendor guarantees there will be "no unforseen side-effects or undesirable consequences" of any of their updates. Again, this could sound like "making excuses" but that's not the point. If the issue is a verifiable bug, then by all means submit a bug report
http://www.afp548.com/article.php?story=20051102133234150
and, also talk to your Apple rep.
Having said that, if the services are critical , you should have tested the update on a staging server first, and even then, properly verified those critical services were running after the update.
Hence the need for proper SOP for mission-critical servers: a known-good, tested backup of the system prior to any update, testing the update on a staging server that can be taken offline at will and is not available to clients even accidentally (except during expected testing), and then SOPs for (or part of your larger SOP) verifying services after applying any update.

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> I am trying to ensure that the colours I see in images at the Save for Web stage preview are what I will see on the web and in other non colour managed environments. Specifically, I'd be grateful to know if the following settings seem right for what I am trying to achieve:
> Preset: JPEG High
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> Optimize selected (but not Progressive or Embed Colour Profile)
I prefer 'Progressive' as that loads an image in 3 stages (low->med->fullRez) and looks better on webpages instead of having images load top-to-bottom like a window shade.
> Convert to sRGB selected
Doesn't hurt to leave it on. Though you said you already converted them before saving for web.
> Preview: Use Document Profile
I think that "Windows (No Color Management)" will display a better preview of what to expect when the image is displayed on a Windows computer (95% of your visitors) using a web browser that's not color managed (ie: 99% of the windows web browsers - are there any?).
> In the past (pre-CS4) I've had problems with images outside of CS3 looking over colour saturated and I want to avoid this now.
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