I had the same problem, previously mentioned in this thread, concerning using an IR remote for a device other than the Panny projector at the same time that the 3D emitter is doing its thing, and not having it work. The device in question was an IR receiver which is used for my HTPC's remote control which is plugged into a USB port. What I did was move the IR receiver to the side of the room where there was a nook, which evidently is outside of the range of the projectors IR beam.
All of my other equipment (receiver, players, HTPC's, etc.) resides in this nook, which is off to the left side of where I sit. So far, all of the equipment that resides there will respond as it should when I point the remote at it.
I realize that this may not work for everyone's setup, but for those that have a place off to the side like I have, it may help to relocate your other equipment there.