In our workflow, we have a few users who are doing design work on Windows installations of IinDesign CS6 (2 in WIndows 7 and 2 in Windows 8). On all four systems, we have noticed that when we open files from packaged folders that contain the Document Fonts folder, that InDesign slows to an excrutiating crawl, which makes working on the document near impossible. We've narrowed down this behavior to the AdobeFnt14.lst file that seems to be a result of InDesign opening the file using the fonts in that folder without being told to. Deleting that file will temporarily fix the problem, but InDesign recreates it when you open the corresponding document and then you have to delete it again.
We use Universal Type Cient for our font manager, but as far as I know, we didn't install any font auto activation plugins.
Other than deleting the font folder, we've not been able to figure out how to stop ID from trying to automatically load the fonts. We'd love to just turn that "feature" off so that we don't have the hassle. I'd rather have fonts missing and turn them on using our font manager, than have ID slow to an impossible crawl whenever we open archived files. Does anyone know how to stop ID from automatically loading fonts from a document fonts folder?