mm maybe your environment is not defined properly,
I share my environment defined in my cygwin user's .bashrc file [CYGWIN environment]
export JAVA_HOME=/cygdrive/c/Java/jdk1.6.0_23/
export JRE_HOME=/cygdrive/c/Java/jre6
export HADOOP_INSTALL=/home/saivulle/apps/hadoop-1.2.1
export PATH=$JAVA_HOME/bin:$JRE_HOME/bin:$HADOOP_INSTALL/bin:$HADOOP_INSTALL/sbin:$PATH
then from cygwin command window
$ hadoop version
Hadoop 1.2.1
Subversion
https://svn.apache.org/repos/asf/hadoop/common/branches/branch-1.2 -r 1503152
Compiled by mattf on Mon Jul 22 15:23:09 PDT 2013
From source with checksum 6923c86528809c4e7e6f493b6b413a9a
This command was run using /C:/cygwin/home/saivulle/apps/hadoop-1.2.1/hadoop-core-1.2.1.jar