Worked out that this plugin replaces the 'global' loop so it includes ALL Custom Post Types and not just the default 'post'.
When plugin is active and CPT created with 'Public' setting these items will show up on your default homepage feed or anywhere you use the general loop. You need to re-work your query_posts to fix.
I moved to another Custom Post Type UI manager and this did NOT do the same thing so I have had to move away from this plugin which is a shame as I really like the [CONTENT] feature.
If this problem could be fixed or at least optional that would be a good move.