Thanks for the report. However I would have liked to have known about the issue before you went ahead and left a negative review, as I work very hard to our users happy.
Additionally, why is it that you were using the plugin for a week before stating that the plugin broke your sites permalinks? That doesn’t seem to add up. It’s possible you installed another plugin, or did something in the interim that broke your site.
When the plugin is installed a custom post type is created, and the permalinks are flushed so it is accessible. No other changes are made to your sites permalinks – so you may want to take a closer look at your site and what might actually be going on under the hood.
Fortunately, I am currently working on a re-write and am taking into account past and current user feedback. I can assure you that the upcoming release is far more customizable.
Appreciate your review none-the-less. I hope an alternative plugin has the requirements you are looking for.
Have a good day.
Evan
Follow Up:
I have just installed custom post type UI and see no noticable conflicts between the two. Both plugins work perfectly fine alongside eachother. Permalinks remain in tact, as expected. If you had let us know about the issue we would have gladly helped you through any sort of conflicts you were running into.