Just set the classpath when you execute the java command... 
#!/usr/bin/perl
# perl stuff here

`java -classpath /cygdrive/c/java/myclasspath myjavathingy.class`

# more perl stuff here

[download]
Also Cygwin in my experience usually doesn't change Windoz variables so you should be safe if you want to set the classpath variable when you open up Cygwin.

In reply to Re: CLASSPATH in perl on windows using cygwin by xorl
in thread CLASSPATH in perl on windows using cygwin by Anonymous Monk

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