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I have mapped buttons on my joystick to the 'Pause' and 'Center' hotkeys, but everytime I restart the App these dont work until I hit the 'Refresh DirectInput' button on the Hotkeys screen.

Very annoying and means I can't just jump into a game.
Is there any way to avoid this?

No way around this?

Are you running any other joystick software, that might be causing the interference?

I have a saitek stick, but I dont use the software for it. All the buttons axis are recognized by windows without a problem.

Are they plugged into a hub, or directly on the system?

Are they plugged in next to each other?

Have you tried turn off any kind of power save feature for your USB ports?

In the "Device Manager" you can right click the "USB Root Hub"(s), that show, and then select properties. On the power management tab, uncheck the box that allows the computer to turn off the USB port to save power (i.e. uncheck the box). Sometimes that has an impact on the connectivity of the devices.

I have a saitek stick, but I dont use the software for it. All the buttons axis are recognized by windows without a problem.

Saitek stick here and the way around the problem is to map with Saitek software.

Hope this helps.

They are plugged directly into the system in non-adjacent slots.
I turned off the power saving as you suggested. This didnt seem to make any difference.

I believe I have discovered the problem, though.
I usually unplug the stick when its not in use (don't want to have those blue LEDs on all the time).

It seems the the Stick must be plugged in and initialized before the TrackIR software is started.
If it is, the center works fine right off the bat. If it isn't I need to refresh.
In hindsight it seems obvious.

Thanks for your assistance anyway, Vincent.

I really have to praise NaturalPoint and yourself for an excellent product and your very convenient, prompt and patient support!

No issues, glad to help out....