We're running PE 6.0 m060 using the DITA application and I didn't have any problems enabling HTML Help. Just installed HTML Help Workshop 3.0 on the server (in the default directory on C:\), ran it once and restarted TomCat. From there I didn't have any troubles creating .chm file. Not sure if that helps at all, DITA might be one of the doc types that isn't affected by what the help says.
Don't know if this will help since we're using axdocbook for HTML Help and not using PE. To get this running from Styler in Arbortext 6.0 M050 I found:
For publishing in Styler, PTC Knowledgebase article: "Compose/Publish for HTML Help" Menu Option is Greyed Out in Windows 7 (TAN 151574)
- Lou Argyres