I had the same problem no matter what I tried. I don't know if this relates to your problem but here is what I did:
1) installed the applicationCore.wsp, Bugdatabase.wsp and the Knowledgedatabase.wsp site templates on environment #1.
2) Created a site based off of both of the site templates
3) Created a new "site template" based off of both of these sites.
4) Copied and deployed these new site templates to another environment and did an IIS reset. (didn't work because the templates that I based these new site templates were not on the new environment.)
5) installed the same application templates as in #1 on the environment #2, and created sites based off of the new templates under "Custom" tab.
Hope that help. The instructions don't give you much information about this.