The problem is that you have created a MIDI player that accepts only files with the extension. On neither Windows nor Mac OS X does LilyPond 2.12.0 update any files with the extension ".midi." These files are created only once, and because of this, LilyPondTool's MIDI player does not respond to changes made by running LilyPond again. From the earliest days of MIDI, the standard extension has been ".mid," and that is what LilyPond writes its changes to. Please make sure that LilyPondTool's MIDI opens only files with the extension ".mid," Thank you!