This is weird. Sounds like your system has some weird corruption.
What happens when you quit PM, does the second icon disappear?
I wonder, are you perhaps not quitting PM but e.g. minimising it? (in that case if you have set your Dock Preferences to not gather windows with the application icon, you will get additional icons (on the far right of the dock) for each window.
If you really get two PM icons at the left side of the Dock, can you tell me what happens when you right click the icons and then choose Show in Finder from the options fly-out menu?
1. Remove the PM icon from the Dock
2. Open PM, one PM icon should be in dock
3. Quit PM, icon should no longer be in dock
4. Open PM, one PM icon should be in Dock
5. Quit PM, icon should no longer be in dock
Does the PM icon show anywhere it shouldn't?