Random 301 Loops with Multi-site

We have a multisite instance running here: http://www.allatsea.net/

We are using sub-directory sites. The two sites are

http://www.allatsea.net/caribbean
http://www.allatsea.net/southeast

Everything seems fine but we occasionally get 301 redirect loops. Occasionally we can reproduce these reliably but eventually it will go away and act fine. There is seemingly no rhyme or reason to it.The problem here is that google webmaster tools finds the religiously, to the tune of 50-100 a day and its never the same URL or even the same patterns of URLs.

Our htaccess file is pretty complex since this site was migrated from a home-grown CMS (all on the /caribbean side) so we do a lot of old to new URL mapping. The 301 looping only occurs on the /caribbean side.

Normally I would chalk this up to some bogus rewrite rules but since its A) seemingly random and B) the problem, on a given url, comes and goes, it feels like something more fundamental.

We have disabled wp-supercache thinking maybe that + multi-site was throwing things off but it did not solve it.

Anyone have any ideas why we might be randomly getting 301 redirect loops like this? Its such a difficult problem to troubleshoot since reproducibility is almost impossible.