I had to do two things to get it to work for me. First, I had to make sure it was pointed to the correct directory for the save games. It wouldn't open because it couldn't find the dialog.tlk file. The first is located in C:/Documents and Settings/[my name]/My Documents/Icewind Dale - Enhanced Edition. The second is located at my installation directory, in this case F:/BeamDog/00794/lang/en_US.
Maybe all you need is to aim the initial installation of EEKeeper to the dialog.tlk file. I'm not sure. I do know that if you've already installed it and used it for BGEE or BGIIEE, all you should need to do is change the EEKeeper targeting by clicking on Settings, then Installation Directory. After that it will ask for the directory where IWDEEs dialog.tlk file is. It's pretty much the same as GateKeeper, ShadowKeeper and DaleKeeper in this aspect.
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Maybe all you need is to aim the initial installation of EEKeeper to the dialog.tlk file. I'm not sure. I do know that if you've already installed it and used it for BGEE or BGIIEE, all you should need to do is change the EEKeeper targeting by clicking on Settings, then Installation Directory. After that it will ask for the directory where IWDEEs dialog.tlk file is. It's pretty much the same as GateKeeper, ShadowKeeper and DaleKeeper in this aspect.
I actually did up some instructions here.