I written a lot of threaded perl code over the last 8 or 9 years, and I've never had occasion to use Thread::Semaphore. To me it seems to be a very complicated (and apparently broken) way to do something very simple.

I would ditch that module in favour of a very simple mechanism.

my $outputSem :shared;

...

                    if ($success)
                    {
                        lock  $outputSem;
                        erase($input_window);
                        addstr($input_window, $buffer);
                        refresh($input_window);
                        $ptr = length($buffer);
                        curs_to_ptr($input_window, $ptr);
                    }

...

sub icb_print
{
    my ($window, $color, $fmt, @args) = @_;
    my $buf = sprintf ($fmt, @args);

    lock $outputSem;
    ...
}
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No guarantees given I cannot see never mind run most of your code, but that simple change will probably fix your problems.