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Why are you advising to use 8.8.4.4 and 8.8.8.8.
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Those are two of googles public master DNS servers. I didn't realize X.X.X.X. was a mask, I thought it might have been in the config as a placeholder and you forgot to change it over to a live IP.
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Do you think about a problem in our DNS
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The cyclical nature of the problem. That normally means something beyond the Linux instance and the web app in question are involved (those things normally work or don't work). Resource contention on the instance or bad code in the app can cause it, but I'm not in a position to trouble shoot those for you (so I'm assuming you've already looked at those possibilities).
DNS is simple to understand as a concept however it's not nearly as simple in implementation. Zones transfer on a schedule between recursive DNS servers, the RR sigs can expire unless roller is running on both servers, which can trigger a problem on the next zone transfer...there's a lot of moving parts to it. It seems like a likely fail point based on the symptom your describing.
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why we don't have a the same problem when we disable the Proxy caching in our router.
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I don't know how much DNS caching your router is doing, nor did I know until a I read your response that you're running internal DNS servers. Squid isn't exactly a DNS resource, it caches web objects which can be anything you find on the internet, which means if your using Squid as a DNS referrer, it's searching through a ton of crap to find the name/ip keypair you're asking it for. DNS has to happen quickly or the server gets buried, which sounds similar to what your experiencing.
The DNS suggestion is just that, a suggestion, based on what I know about your problem which is a couple dozen words on an internet message board. I'm happy to bounce ideas off you but if you feel you need a professional engineering assessment, you need to hire an engineer. Linuxquestions is not a substitute for on site expertise.