Do I infer from Mellis's post that "Run.bat" is an alternative way to get into the Arduino development environment?
FWIW, I'm using Arduino.exe (010) on an XP machine, and it seems happy enough. No Processing. No cygwin. Java RTE 1.6.0_03
(Wow! Busy thread! This used to say "previous post", 'cause when I went to write it, none of the several intervening posts were up yet!)