it doesn't make sense for flush() to timeout, since it's purpose is to ensure that the output has been sent.
You just need to flush more often in your scripts if you are really having to wait 100 seconds for flush to complete.
Just as a sanity check, when it takes 100 seconds, how much data are you outputting from the page?

well, i use it in a chat script. the output most often is only a few hundret bytes, flushed about every second. it seems that sometimes (may be when the client disconnected) the flush 'hangs' (flush takes between 300-1500) seconds. it would be good to have a command like bool flush(int timeout), so the chat client could be kicked if flush would take longer than say 30 seconds.
my loop looks like
while (!connection_aborted() && !$do_end)
{
...
flush();
usleep(0.75*1000000);
}