Nginx – added a new domain to the same ip, new domain rendering first domains wordpress blog

If those directories need to be identical, could you put them on another server and mount them remotely via NFS?

You haven't ruled out DNS just yet, because nslookup is not the same as nginx or PHP performing the request. Watch DNS requests out to see if any of them are patently silly.

Whenever anything is unexpectedly slow (HTTP request, initial ssh connection, etc), but only slow at first, it's generally a reverse DNS request that's timing out.