An array of perplexing server problems

Hi, Gang!
We have just installed RoboHelp Server 9 and are publishing to it from RoboHelp verion 9.01.232 and we are seeing bunch of consistent problems.
I can publish to the server (WebHelp Pro project) yet when I attempt to preview the help through the server admin tool (via the Projects pane), it loads nothing but a blank page. The same is true if I attempt to view the hosted help system using a browser from outside of the admin tool. This exact same help system opens just fine manually using a browser.
If I attempt to delete a project (delete on the Projects pane, click Apply) the help projectis still there if I refresh the Projects pane by reloading the pane or by logging out and back in to the Admin tool.
Attempting to publish a second WebHelp Pro project seems to publish successfully (RH reports success) but the second project never appears; only the first one (even if I've deleted the first project repeatedly).
If I publish a FlashHelp project, it will display; however, it exhibits the same behavior as the WebHelp project in that I cannot delete it.
The Troubleshooting pane of the Admin tool shows "No default window for the [project name] project," and "No default project as been identified." Not sure about the former, but the documentation states that the server uses the topmost project as the default project so other than placing a project on the top I'm not sure how I specifiy that the only existing project is to be the default one.
Sometimes, rebooting the entire server will cause the Admin tool to display the correct reality (i.e., it will update to reflect deletions and new uploads and show what projects really exist), though the reboot only corrects the display issue in the project listing and I still cannot view the WebHelp Pro project or reliably delete or add new projects.
If I create a FlashHelp Pro project, it displays successfully using the Projects pane preview.
We have reverted the server back to a snapshot and reinstalled everything and this behavior does not change. Here are the specific versions of Java RE and Apache Tomcat that we are running.
1.     Java Runtime Engine, jre-6u23-windows-i586-s.exe
     Apache Tomcat Server, apache-tomcat-6.0.14.exe
I welcome any suggestions for getting this system to behave consistently and reliably.
Many thanks!

Hi Rocky. I'm UK based so working on a different time scale than you and John. More than happy to help out if I can though. Initially I can't offer any more advice than what John has already offered. However I would backup John's suggestion to delete all the folders on the server. It often fixes problems of this sort. If when you email John your log files you also email them to me, one of us can take a look at them and pass them on to the relevant people if necessary.
  The RoboColum(n)
  @robocolumn
  Colum McAndrew

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