I am using WindowsXP and I have the same behavious. That is, a new window for each member in eclipse and it is driveing me crazy. I took a look at the regestry and it is set up like your example [Open("%1")].
Each time I select an object for editing in Eclipse a new instance of Pl/Sql opens and asks me to login to the database. How can I set the tool to use the existing instance or add parmaters to eclipse to use the existing instance?