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It isn't at all unusual for Google to be confused when it finds a new site on the same IP, have been seeing this for many years. It usually sorts things out in 2 or 3 weeks. [webmasterworld.com...]
We relaunched a batch of sites with different ccTLD's with the same or similar content, that were previously cached correctly. They sit on the same virtual server [ Amazon Elastic ], so I assume they have the same IP address, but I'll double check.
They are not caching correctly now.
.com and all other ccTLD sites are now caching as .com.au . In the previous month, they were all caching as .co.uk. It's quite a dance and the traffic had previously tanked in the cut over due to duplicate content [ canonicalization issues , which are now resolved ].
A search around the forums brings up many theories, and many instances similar to this, but the above post, is what I want to believe. That is, that it will resolve in time.
Most folks don't come back to tell the tale after things resolve, so it would be good to get some testimony from members who have experienced this phenomenon and how they believed it resolved, or that they fixed it.
Is anyone able to throw some light on this to help others going through a similar experience.
The obvious "explanation" would be that the two domains share the same IP address (do they?) and something in the server set-up is technically incorrect. Alternately, there could be a technical bug on Google's end - they used to happen years ago with shared IP addresses.
If the sites are not on the same IP address, then I'm out of ideas except for a total Google bug. If that's what it is, Google usually fixes them pretty quickly. They seem to be related to corrupted areas when they move data around their servers.
.com and all other ccTLD sites are now caching as .com.au . In the previous month, they were all caching as .co.uk
Google's cache display is handled separately from the search display, and caches and serps are often served from different data centers.
Do they have any individualized content? Distinctive spelling? Place names? Currency values? Local news?
Do they contain any different information for their different locations? Are the inbound links from independent sources and appropriately geo-local?
Any other reasons for their being on separate ccTLDs?
Are they heavily interlinked?
are you using any link rel elements?