You could possibly use threads and make the main thread the work thread and a child thread a 'watcher' thread, or vice versa. It would basically go something like this (untested pseudo code):

use threads; #lets us make threads
use threads::shared; #lets us share variables between threads

my $job_done : shared = 0; #allow the main thread to notify the child 
+thread it is done.

sub watcher {
    my $error = 0;
    until ($job_done) {
        if (error windows appeared) {
            $error = 1;
        }
        sleep 1; #use Time::HiRes qw(sleep) or select(undef, undef, un
+def, 0.5) if you need less than 1 second testing
    }
    return $error;
}

my $watcher = threads->create \&watcher; #start the watcher thread
system(call the program); #this will tie up the main thread until it f
+inishes
$job_done = 1; #this should let the thread exit on the next loop
my $error = $watcher->join; #clean up the thread and get it's return.
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