Running RoF as Administrator, along with the TrackIR software and any controller software, seems like the way to go -- It almost ought to be the default Windows setting IMO.
One other procedure, to avoid any possible key command conflicts, for RoF or any other software, is to assign the TIR commands directly to buttons, rather than to keys. The default F-keys for TrackIR commands will probably already be assigned to in-game commands by just about any game that would use TrackIR - a conflict waiting to happen. Direct button assignment in the NaturalPoint software is for the specific profile, e.g., the one used for RoF - it's easy.