It may have been a conflict with the WP Alchemy Meta Box class:

http://www.farinspace.com/wpalchemy-metabox/

Content saved in meta box text fields generated by the class are stored in custom fields, and when the Save button is pressed that content was being saved in the main TinyMCE editor. Changing the priority in Relevanssi fixed the issue.

Also, I'd be interested in a description on how to reproduce the bug.

Drop me an email to mikko at mikkosaari.fi, if you get your write-up done, so I can add a link to it on Relevanssi.com.

While working with the custom fields indexing option I encountered a bug that would automatically add custom field values in the post content during the save_post action.

I dug into the code and isolated the issue to Line 2322. I was able to fix the problem by setting the priority and accepted arguments parameter of the relevanssi_edit function on Line 39 of relevanssi.php:

add_action('save_post', 'relevanssi_edit', 1, 1);

Thanks for all the time and effort you've put into this plugin, I'm planning to do a nice write-up on a how to use Relevanssi to create search filtering forms similar to Kayak.com (except probably not AJAX unless I'm feeling ambitious)

http://wordpress.org/extend/plugins/relevanssi/