Most ECU's limit engine RPM by shutting down injectors and when you bounce up against the RPM limiter, it can feel quite violent. What you have is a an engine that is running full bore and then the ECU starts shutting down injectors and it feels like a engine miss (which it is) and feels like somebody is back their pulling off plug wires.
If you do not feel this banging and dropping of cylinders when running at 5500 RPM then I doubt the ECU is casuing this and your prop just has this engine limited (by design) by load only. Prop pitch is one way to limit engine speed, prop diameter, number of blades, prop material all have an effect on how fast an engine can run at WOT but if designed / recomended to run at 5500 and that is what you are getting, then I would be happy. This unless you are suffering at some other performace aspect that you would like to improve such as range or time to plane?