If I'm understanding your question, you have ThinApp'ed a font management program and included various fonts inside the package - and when you run the font manager you are expecting the packaged fonts to be visible to other applications on the system?

ThinApp doesn't do that, instead any virtual fonts (those inside your package) will only be visible to application running in the same namespace. So you would either need to package the apps that use the fonts together with the font manager, or use AppLink to link them together at runtime. There is no way for a system-installed app to see fonts from a package, this is by design.

Read more at: http://communities.vmware.com/message/1522244