Programs on windows are supposed to use the %appdata% folder to store their settings, so %appdata%\MComix in this case, not %homepath%\MComix as it does now.
This should be possible to achieve by using the appdirs module
Win 7 (not roaming): C:\Users\<username>\AppData\Local\<AppAuthor>\<AppName>
Win 7 (roaming): C:\Users\<username>\AppData\Roaming\<AppAuthor>\<AppName>
Most of the time, the settings are stored in the roaming profile. I'm guessing the local profile is for settings that would vary from machine to machine (commands specified in open with -> edit commands maybe?)
The user directory has been moved to %APPDATA%/MComix.