Marketpress plugin - dropping permalinks for the site

I recently installed the Marketpress plugin and after about an hour it drops my permalinks structure. I can reset this manually but it consistently happens until I disable the plugin. It's happening throughout the site and on all posts and custom posts. I did rename the /store/ to /bookstore/ within the settings but would this have caused the issue? It's a shame that I spent hours setting up the pages and products to now have to disable the entire project. I am using WP3.61 and the latest on all plugins elsewhere. Does anyone know of a fix that would resolve the permalink issue at all?