Hi Johannes,
I don't fully understand what you are trying to do.
The PPT is designed to be a optical/intertial hybrid system, so clearly for a 6DOF pointing device we would recommend to use an Intersense InertiaCube2 (with wire) or InertiaCube3 (wireless) in combination with one tracked LED marker (wireless).
On the other hand, if you want a handheld pointer (i.e. a 5DOF tracked device), you can indeed use two LEDs for this. The PPT itself does not give you their identities (which could explain why you saw things 'flipping' like you reported), but typically they are mounted on the handheld device at a fixed distance, which is all the information you need to make it work.
Please contact me directly at
pusch@worldviz.com and we will provide you with a sample script for such a pointer application.
Have fun!
The WorldViz Team