The cross-platform version of POPFile v0.21.1 does not work out of the box under cygwin. This is due to a bug in the DBD::SQLite package, which does not recognize UNIX-style filename paths when built in cygwin using the standard CPAN installation system. A bug report has been filed for the DBD:SQLite module and is available here.
Should you find anything in the documentation that is incomplete, unclear, outdated or just plain wrong, please let us know and leave a note in the Documentation Forum.