Autoflush on the WRITE filehandle in A seems more likely to be the problem. In newer versions of Perl you can use:

use IO::Handle;
# ...
WRITE->autoflush(1);
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In older versions you should use:

$oldfh = select(WRITE);
$| = 1;
select($oldfh);
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Update: bluto's right, IPC::Open2 does this for you. I usually just use pipe, which doesn't.