sub StopCheck{
    $| = 1;
    print "\n" or die "STDOUT gone away";
}
[download]

Problem solved I call this subroutine with each iteration of my programs main control loop. The die is redundant in Apache/UNIX as it dies when you print anyway. Works when the user presses stop or navigates away from the page. As it's per filehandle I don't think you have to turn buffering back on.

Also has the added benefit of keeping the connection alive

Thanks for all your help.
Update: Zuqif suggested I adapt this sub to create a progress bar in the browser. Some magic todo with browser refreshing I think is required