In Windows, FreeMind stores its settings in getProperty("user.home") + ".freemind". That is different from the customary Windows location for application data, which is in Windows Vista typically ~\AddData\Roaming\FreeMind for an app called "FreeMind", without the leading dot and with proper capitalization, on the model of what most applications do. Above all, Java's "user.home" is plagued by a long-standing Java bug that is unlikely to get fixed any soon: the Java determines the value of "user.home" by going to the location of user's desktop and stripping off the last part. In a Windows network environment that uses shared desktops, each user has the same desktop folder, which leads to FreeMind using the same settings folder for each of the users, which is wrong.
Fixing this bug requires proper research that I have not done yet. Going to getProperty("user.home") + "\AppData\Roaming\FreeMind" does not work, as getProperty("user.home") is plagued by the Java bug.
Concerned FreeMind versions: 0.9.0, 0.8.1, 0.7.1, and all earlier.
Workaround: I do not know any, but maybe there is one.
Other bug reports similar to this one:
.freemind relative to 'desktop' directory..., 2009-05-25
home directory incorrectly read, 2008-04-13