I don't have ready access to a Windows partition with LyX 2.1 any more, so I'm winging this a bit. I noticed your path to lyx.exe contained "cygdrive":
> $ /cygdrive/c/Program\ Files\ \(x86\)/LyX\ 2.1/bin/lyx.exe -x reconfigure By any chance does that mean you have LyX installed on a machine running Cygwin? Years ago I had problems with reconfiguring LyX because Cygwin had a (broken, as I recall) version of latex that appeared on the command path ahead of the MiKTeX version. If that's the case for you, moving MiKTeX's bin directory ahead of the Cygwin bin directory on the system command path might help. (I would put LyX's bin directory ahead of Cygwin's as well.) Paul
