Interesting... I don't know whether this ever worked properly. This seems to be an issue with spaces in the Path, but also with cygpath conversion.
Can you please comment out the entire CYGWIN case statement in the cassandra script.
Then add this into the cassandar.in.sh after the initial two initializations of these variables:
cygpath -s -m "$CASSANDRA_HOME"
cygpath -s -m "$CASSANDRA_CONF"
Finally, change the CLASSPATH setting variable in the for loop at the bottom to:
Let me know if this is too complicated and I can see about getting you the raw scripts.