ManaUser,
WMP is by Microsoft so it shouldn't cause any complications in Windows itself.
As an alternative, why not try running Virtual PC instead? That way, install anything you want on the Virtual PC and have it not interfere with your current computer's O/S. Use it to install the AMV Convert Tool, install any codecs you want and convert your videos. All this in a virtual environment so it won't interfere with your existing computer's operating system. Then you can save the converted file onto your 'real' computer.
Hope that helps.
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