Wizard - 7:25 am on Aug 24, 2006 (gmt 0)

Are you sure that your scripts are working properly? You said you copied the code and made static HTML and it started ranking well. Maybe the script does something wrong, and this is the reason, not the directory - except the fact that content in this directory is generated dynamically?

Use Live HTTP Headers or similiar tool to check if HTTP Headers for dynamically generated files are made properly - for example, some CMS systems add redirects which would kill Google ranking.

And adding links from other domains to your deep pages (saying deep pages, I mean pages other than home page) is essential.