Windows CMD automatically appends some 'know extensions' to files when trying to run them. In this case it's changing your truffle command to truffle.js (instead of ...\node\bin\truffle.cmd) because a Truffle.js file exists and .js is a 'known extension'.
CMD's 'know extensions' are stored in the PATHEXT environment variable, which in my machine contains: .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC
So, in my case, I just removed JS extension in the current console.
set PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JSE;.WSF;.WSH;.MSC
Or, I remove it system wide.
setx PATHEXT .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JSE;.WSF;.WSH;.MSC
(Please note setx does not update already opened consoles until you restart them.)
truffle.cmd. – Ismael Jul 04 '17 at 18:01