Running multiple instances of msys tools concurrently (especially non-interactively via a service or scheduled task) causes paths in some environment variables to lose their leading slash and thus become "corrupt".
Tested with msys-base 2013072300.
A Python script is attached that demonstrates the problem. It spawns two bash processes per second for 10 seconds that print out the environment to a file and check whether $HOME is readable. Any failures get logged to msys_test.stdout.log.
HOME=/c/Users/buildbot TEMP=/tmp TMP=/tmp TMPDIR=/tmp PATH=/c/Perl/bin:/c/Python27:/c/Windows/system32:/c/Windows:/c/Program Files (x86)/Git/cmd
HOME=c/Users/buildbot TEMP=c/Users/BUILDB~1/AppData/Local/Temp TMP=c/Users/BUILDB~1/AppData/Local/Temp TMPDIR=c/Users/BUILDB~1/AppData/Local/Temp PATH=c/Perl/bin:c/Python27:c/Windows/system32:c/Windows:c/Program Files (x86)/Git/cmd
See https://sourceforge.net/mailarchive/message.php?msg_id=31374034 for more details.