I'm running into similar issues like http://stackoverflow.com/questions/22462665/is-hadoops-toorunner-thread-safe, the author's observation seem to make sense to me. However when I checked the hadoop github trunk I found the issue still not fixed.
Chris Nauroth further investigated this issue, here's his quote:
The root cause is that commons-cli OptionBuilder is not thread-safe.
According to this issue, commons-cli doesn't plan to change that and
instead chose to document the lack of thread-safety.
I think we can solve this in Hadoop, probably with a one-line change to
make GenericOptionsParser#buildGeneralOptions a synchronized method.
I'll soon upload a patch for this