It might be interesting to see the log files at the time it screws up. But without access to your actual ftptelnet server, this is pretty hard to test.

I would at least try fixing the newlines so you're not sending CRLF to the cmd() function - it expects only the \n. And make sure there are no empty lines. i.e.:

    while(<>) {
        chomp;
        next if !length;
        @lines = $t->cmd("bin/dsjob -jobinfo $project $_\n");
[download]

Maybe add an explicit timeout option to the cmd() function as well.