is it possible that each call of cmd uses a new instance of your shell? try doing it all in one big command

my $cmd = <<_COMMANDS_;
export SYBASE="/usr/local/sybase/OC"
export AUTOSYS="/usr/platinum/autosys"
export AUTOUSER="/usr/platinum/autouser"
export __std_err_file=/dev/null
export __command=NIL
export AUTO_JOB_PID=0
export AUTO_JOB_NAME="myjob"
export APP_ROOT=
autorep -q -J myjob#init#t
_COMMANDS_

... $ssh->cmd($cmd);
[download]

if nothing else it's easier on the eyes.