Alias Files and Bookmark Files
The long and short of it is Apple has moved away from “alias files” in recent years, and now favors a format they call “bookmarks.” To users, the files behave the same way, and Apple continues to call them “aliases” e.g. in the Finder when it offers to make an alias to a file. However, the older system service for “resolving an alias file” does not work on bookmarks.
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The problem was compounded at some point, maybe as recently as OS X Yosemite, when Apple started aggressively converting old alias files into bookmarks. So even if you had an old, functional alias to a folder in your script tree, it may have recently stopped working in FastScripts because Apple converted it … helpfully … to a bookmark.
