Hmm. So the alias file is really called "numbers files f alias" exactly? You don't have any funky FinderPop "---x" suffixes?
And the alias really does work?
Does the alias show up expanded when you right-click a file in the Finder? (The menubar popups are handled by the FinderPop daemon which starts early and builds its menus early too...) Could it be that the disk it's on wasn't mounted at the time FinderPop built its menus?
An easy way to check this would be to force FP to rebuild it's menus. Either go to the prefPane and turn FP off and then back on, or open up the FinderPop Items folder and create a new folder there, and then immediately delete it (Command-Shift-N, Command-Delete) - this will cause the modification time of the FinderPop Items folder to be changed, and FP will rebuild its menus for the folder the next time it's invoked.
FP will print something to the Console (Applications -> Utiltities->Console.app) if it finds something funky while scanning files. (But an unfollowable alias isn't considered 'funky' IIRC.)