Here are some observations I made while investigating this ticket :
First, sorry for the novel >.<
I open FileTypes, I select the Be Application Mimetype, set the preferred app. to None and Tracker's item disappear from the menu, as mentioned.
I went to FileTypes's source code (PreferredAppMenu.cpp) and requested the message listing the supporting applications message to print on stream. I was puzzled to discover it wasn't returning Tracker. So I found out Tracker was first shown simply because it was the current Preferred App. So changing the preferred app had for effect to remove Tracker from this menu on next update (since it wasn't even listed as a supporting app)
Next, FileTypes > Application Types. I select Tracker, remove its support for Be Application Mimetype, and re-add it. Close (and save) the window. Back in FileTypes main window, I can now see Tracker in the menu for the preferred App of Be Applications. Selecting None doesn't make tracker disappear now. And the supporting Apps message returns Tracker now.
Next, I close and reopen FileTypes. The "fix" is still effective, the support of Be Applications files from Tracker is still recognized.
Next, I reboot. It returns to the old behaviour where selecting None makes Tracker disappears from the preferred app. menu.
So, there must be something wrong with the way the mime database is loaded on boot. I'm trying to figure it out, but can't promise anything, since I'm learning how it works while trying to fix it :)