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The TrackIR does not appear in the list of Controllers under Game Controllers and does not auto-load when I start a game. It does not work in a game unless I start the software before I start the game.

I have the latest driver and software. I am using the 64-bit version of Vista Home Basic (although I had this exact same problem with XP 64-bit) running on an Asus A8R32-MVP Deluxe motherboard.

OK, this is all normal.

When the TrackIR installs, it is listed as a USB device, in the Device Manager.

You need to have the TrackIR software runnning, before you start a gaming application.