On Wed, Apr 27, 2016 at 02:33:26AM -0400,
 digen <di...@protonmail.com> wrote 
 a message of 169 lines which said:

> Any inputs on debugging this problem will be much appreciated.

The usual stuff:

1) Is the machine hosting the resolver overloaded? top, for instance

2) is the link to the Internet overloaded? Check your Cacti (or other
software) graphs.

3) Routing problem? traceroute to the name servers. (Don't try ping,
microsoft.com's servers appear to refuse it)

4) An easy way to test DNS performance issues is with a dedicated DNS
test program like check-soa
<http://www.bortzmeyer.org/check-soa-go.html>:

% check-soa -i microsoft.com 
ns1.msft.net.
        2620:0:30::53: OK: 2016042614 (22 ms)
        208.84.0.53: OK: 2016042614 (40 ms)
ns2.msft.net.
        208.84.2.53: OK: 2016042614 (24 ms)
        2620:0:32::53: OK: 2016042614 (25 ms)
ns3.msft.net.
        2620:0:34::53: OK: 2016042614 (22 ms)
        193.221.113.53: OK: 2016042614 (40 ms)
ns4.msft.net.
        2620:0:37::53: OK: 2016042614 (25 ms)
        208.76.45.53: OK: 2016042614 (40 ms)

% check-soa -i sony.com     
pdns1.cscdns.net.
        2620:74:19::33: OK: 2011041474 (19 ms)
        209.112.114.33: OK: 2011041474 (34 ms)
pdns2.cscdns.net.
        69.36.145.33: OK: 2011041474 (23 ms)
        2001:502:cbe4::33: OK: 2011041474 (27 ms)
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