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Make sure Pan Views are enabled.
The default keypress for this is F9, which is also the default Hotkey for TIR enable, so you may have to change that in TIR first. Then hit NumPad 5 for Centre View. Does that fix it?

Well, I thought I'd test out your original theory that it was related to the trackir and disabled it in the Config.ini and it made no difference at all so I don't think the above will have any effect. Thanks for trying! Any other ideas?