We ran into an issue with one of our clients using MarketPress Lite in which MarketPress would flush and regenerate the WordPress rewrite rules in every init.
After some troubleshooting, we narrowed it down to the "install" function getting called every init, which adds an action to flush the rewrite rules. This occurs because it's looking for the 'mp_version' value within the 'mp_settings' option, but never sets that key and instead only sets the option 'mp_version' in all future occurrences.
I've attached a link to the patch I've created in our github mirror. It includes a simple diff to see what changes were necessary to occur. Changes to the version number and description in the header can be ignored, as these are used for our internal purposes.