Not sure if any of you devs realized it, but certain cross-platform apps (e.g. The GIMP, GnuCash) will store settings to the Cygwin home directory (%home%) if the Cygwin DLL is in the path. These programs may not even store the info in %appdata%, favoring %home% exclusively.
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GnuCash uses %HOME% regardless of the presence of cygwin, actually. It's the method I use to point its files to the Profile directory. It also honors %TMP%.
formerly rayven01