Now that you have it working, I wonder why you bother writing a bash script file to be executed in a separate system call, rather than just doing the "cvs" command itself via a perl system call. Seems like your script could just be:

chdir $wrPath;
my $failed = system( "cvs diff >> $reportsPath/diffReport.txt" );
if ( $failed ) {
    warn "cvs diff returned non-zero exit status $failed\n";
}
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If the rest of the script does stuff that depends crucially on what your current working directory is (before and/or after running "cvs diff"), you just need to add:

use Cwd;

my $origpath = getcwd;  # before doing 'chdir $wrPath'

...

chdir $origpath;  # after doing 'system( "cvs diff ..." )'
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