CustomPress Wierdness - Page Not Found

I'm having some serious trouble with CustomPress. Two main issues on this site:

Three initial considerations:
1. "News" is a custom post type created with CustomPress
2. I am using LoopBuddy from iThemes to control the layout of the custom post type data
3. I have had these issues before on another site as well using LoopBuddy and CustomPress

The Two Issues I'm experiencing:

1. I have the news items paginated, 5 at a time. Randomly (?) moving to another page throws a page not found error. I am using WP-PageNavi for the nice page number links, but this issue existed prior to installing that plugin. Deactivating and reactivating CustomPress seems to solve the problem. But obviously that's not a good solution since it keeps happening.

2. After I added a bunch of news items today, when I click a news item, it will throw a page not found error... although the URL is correct in the address bar. Also, this happens for ALL of the custom post types on the site (projects, news, bible institutes, missionaries... all were created with CustomPress). For this, I've found that if I set permalinks to default and then back to post name (which is what I want it to be), that works most of the time. Again, this is not a good solution since it keeps happening.

I appreciate ANY help on this. Thanks!