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Calibre stores settings in C:\Documents and Settings\username\Application Data\calibre (or the equivalent depending on the variant of windows). With the latest calibre releases there is an option specify this via an environment variable but that is not set by default. This option was added to support mobile calibre installations.
I am converting all those format you mention without issues on XP Pro +SP3 which I thought was fundametally the same as the MCE variant, so cannot guess what your problem might be.
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