Apparently, the file input plugin does not work on Windows. Logstash keeps reloading the same lines over and over, thus duplicating documents in the output sink. (See LOGSTASH-429. In other words, the tailing process that follows new lines in the input file is broken.

The solution is simple: download the zipped patched Ruby Filewatch from Github, and unzip it into logstash/vendor/bundle/jruby/1.9/gems/filewatch-0.5.1/lib folder. (There are two new files: JRubyFileExtension.jar and filewatch/winhelper.rb.)