Oh my head hurts thinking about all those low-level details, and I'm not sure I'm correctly interpreting your problem. But I thought you might like to read perldoc -q filehandle which has some code for dealing with blocking filehandles. I used the following code to test for anything in the pipe, before trying to read it. That way, you read if there is something there, else move on to the next.

#see which filehandles have output from perldoc -q filehandle 
      $esize = pack("L", 0);
      ioctl(\*ERROR, FIONREAD(), $esize) or die "Couldn't call ioctl: 
+$!\n";
      $esize = unpack("L", $esize);
      print "esize-> $esize\n" unless ($esize < 1);

      $rsize = pack("L", 0);
      ioctl(\*READ, FIONREAD(), $rsize) or die "Couldn't call ioctl: $
+!\n";
      $rsize = unpack("L", $rsize);
      print "rsize-> $rsize\n" unless ($rsize <1);

     #get the output from bc 
     if($esize > 0){sysread(ERROR,$error,$esize); $errortot = $errorto
+t.$error}
     if($rsize > 0){sysread(READ,$answer,$rsize); $answertot = $answer
+tot.$answer}
    } until(($esize > 0)or(($rsize > 0)and($rsize < 4060)));
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