Question: I've got a single domain. I moved my nameservers to AWS R53 yesterday. These are A record, alias'd to my ELB > EC2s.

However, occasionally, and mostly on subdomains I get drop out. It just could not be found.

Also, what appears to only happen on subdomains... I get really slow responses. This is not EC2 related, the www. responds super quick. And my carbon copy site works fine elsewhere, also pre-R53 loaded in normal speed.

I've done live HTTP headers and monitored logs, nothing hits the box until it visibly begins loading. So, it's obviously in the DNS realm. I'm not a great packet sniffer, so looking over Wireshark/Ethereal logs, I can only see whois and then standard queries to domain. Bit messy to work out what's going on.

Any advice or pointers in which to try and follow this problem up would be greatly appreciated.

Answer: 
To confirm that this is a DNS related problem, you can define your subdomains in your machine hosts file (`/etc/hosts` under Linux and `C:\Windows\system32\etc\hosts` under Windows). If you get a quick response in this case and slow response in the previous case, this confirms that you have a DNS problem.

If so, you need to check your DNS server configuration. This also can happen if you configured your machine with primary **faulty/slow** DNS server and secondary **working/fast** DNS server. So, you will not get the resolved name before timeout occurs waiting for the 1st server.
Could be that queries still go sometimes to OLD nameservers. Nameserver addresses May be cached for some while by intermediate DNS resolvers.