The qpid-server bash script passes it's arguments through to qpid-run, which allows various arguments and options to be set for such things as using external classpaths, setting options required for the management modules etc etc (long list !).
However, the qpid-server.bat script has not been kept in step and lags behind significantly in terms of features. It needs to be udpated to support the same set of features that the qpid-run script provides. Note that
QPID-14 is currently outstanding which would make updating the bat script easier to complete as it'd provide a list of features to match.
Note that it's been reported that the QPID_OPTS param is not picked up by the qpid-server.bat script. QPID_ARGS works ok, but only useful for passing options to the server's main class.