Bizarre registry swapping between two cloned sites on localhost

I just duplicated a site on my localhost. Different Drupal install, different database, different virtual domain name, same localhost. The sites are a clones in every other way. I have done this before by simply dumping and re-importing the database and changing all occurrences of the source domain name with the new domain name using a serialized string search/replace. So this has never been a problem in the past though that was with smaller sites. This time the difference is that I have a lot more modules installed, including ones that may be caching and hiding information somewhere I’m not familiar with.

I have followed exactly all the prep instructions for doing this like putting site in maintenance (though it’s not production), clearing cache, and even many disabling inessential modules.

So am not sure whether to post this in Authcache or Memcache or both, because I’m not sure what’s causing the issue.

First the issue that I was getting many bootstrap fatal errors like one with "authcache_views_plugin_display_extender and something with the drupal user entity class not being found. Basically too many to put here. In brief I was lead around to trying Registry Rebuild and this is where things get weird.

When I rebuild the registry and clear cache on the clone I can then it loads ok. So then I go back to the original site it gives me various fatal require_once errors. If I rebuild the registry on the original site, the cloned site goes back to showing fatal errors. So rebuilding registry on one causes changes all the file paths on the other site to the other site's modules directories.

I looked into the registry tables of both original and clone and they indicate the correct module paths, which is why this seems like it could be cached somewhere.

Another odd thing is that drush core-status on both sites show everything normal except that the user is Anonymous.

I’m using Drupal version 7.31. with php 5.4.24

Any help would be much appreciated. Believe me, I've tried to avoid bothering the community on this, but I've hit a wall on this one.