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With both my old drivers and the new ones mouse emulation is only working when either the TrackIR or Mouse Emulation software windows have focus. As soon as anything else has focus it stops updating the mouse position. The gauges on the mouse emulation utility are still moving.

How do I get it to work at all times? (including on the windows desktop)

The mouse emulation application that we include, with the TrackIR software, is only designed to be used within a gaming application, it isn't desgned to be used on the system desktop.

Using Mouse Emulation in Games

The basics are as follows:

Load the TrackIR software.
Load the TIRMouse.EXE file that is located in your TrackIR installation folder. C:\Program Files\NaturalPoint\TrackIR for example.
Load the game you wish to use and be sure to have the mouse look option enabled within the game.
With mouse look turned on you should be able to use the TrackIR now.

Seeing as this is intended to be used for games that are not trackir enchanced how does it tell that I'm running a game and enable the mouse emulation? i.e. How can it tell the difference between window 1 which is a game and window 2 which is something else? Or does it assume anything running full screen is a game and anything else isn't? (Which would mean if your game runs in a window you are out of luck).

A gaming application and mouse look mode are generally using directx, in some form or another. The mouse emulation application is tied into directx.

Thanks for the info, I'll look at implementing my own version in c# using the OptiTrack SDK

(FYI: What I've got here are two game windows which I'm hoping to be able to switch between by looking at them. I was hoping a combination of mouse emulation and the tweakui select on mouseover options would more easily accomplish that )

I do use the trackir for more normal gaming as well and that's fine