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When you launch the viewer or editor from within calibre, they are not launched using the standalone programs, but rather using the worker process, calibre-parallel.exe. This allows integration between calibre and the tools it launches. I'm not a windows user, but surely there must be some way to configure its docking to not group some programs.
@davidfor: The second calibre-parallel process is used to do background processing on another CPU in the editor, I believe I talked about that in another thread.
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