Here's how I got it working well on my Windows 2008 Server Standard x64 machine. Going off memory here and I'm not saying this will fix any of your issues.
* Setup the OS per the directions here: http://www.win2008workstation.com/wordpress/
* Logged into Admin level account
* Installed PMS 1.04, let it install Java
* in Control Panel \ Admin Tools \ Services I set the following to Automatic: SSDP Discovery and UPnP Device Host.
* Disabled screensaver and sleep/hibernation options
* Copied PMS to the Start \ Programs \ Startup group so it will auto-start with this account (was unable to get it running as service due to x64 or other issues)
The only issue I encountered was the screensaver/require login option which was enabled by default. Whenever the screensaver/login would appear I'd be unable to connect to PMS. Login, could connect to PMS. Even though the admin level account was NOT logged out specifically just having the login window seemed to disable it from connecting to the PS3 for whatever reason.
I'm no server admin and really only installed 2008 as I had a valid license via MSDN subscription and wanted to try it and was considering trying my hand at Exchange so I can centralize all of my Outlook features to sync with my desktop/laptop/WinMobile Fuze (how cool would that be?). After monkeying with Server 2008 for a couple hours I actually wish I'd used Windows Home Server as it'd likely have been dumbed down for the type of user I am, though it doesn't support Exchange. I'm assuming WHS has nice wizards and pre-configured services/etc. setup for the standard home server user, which really describes me. Multi-PCs in a home environment requiring a dedicated machine to run as the media/file server and hopefully mail server.