If you want to time out reading the output of an external command, then you really need to use     open(PIPE,"$command |")... and not backticks.

Besides the problem you have already noticed, signals in Perl still aren't reliable and so have about a 2% chance of breaking Perl each time you use a Perl signal handler. So it doesn't take very many invocations of signal handlers before you have a pretty good chance of your script behaving unpredictably.

A better solution would be to use select on a PIPE that was opened.

I changed the backticks to 'open' and all seem to be fine. thanks much.

It sounds like perl isn't getting a chance to close the pipes from the backtick'd commands and is leaking file descriptors. You might be better off doing a fork/exec yourself, or perhaps using IPC::Open2 or IPC::Run and explicitly closing handles yourself.

Are there any variables or something that I can look at to confirm this. I know there's the $^F, but it's of no value.

If you've got something like lsof available you could use it to check from outside your program. Inside your program the only way I can think of offhand would be to open something (/dev/null or the like) and then use fileno on that handle and see if the file descriptors are steadily increasing (which would probably mean you've got a leak).