I've managed to solve this now using awk instead. I know its not perl but for those interested here is how I did it.

#!/usr/gnu/bin/gawk -f
BEGIN {
    OFS=FS=","
}
{
        com="xchop -d, group.csv " $1
        while ((com |getline res) > 0) {
                if (split(res,arr) > 1)
                        print $2,arr[2]
        }
        close(com)
}
[download]

Thanks Jim