Permalinks, Custom Post Types and 404's

I am having some major problems with permalinks and custom post types. I would like to use /%year%/%monthnum%/%postname%/ as the permalink structure. When I save that structure on the permalink settings page, the regular wordpress pages and blog posts show up fine. However, the custom post types return a 404.

Here’s the kicker; when I go and re-save this same structure on the permalink settings page, the custom post types and blog posts work fine, but now the regular wordpress pages return a 404 instead of the custom post types.

I don’t much of any PHP and have scoured the forums and web for hours looking for a fix that I could understand and implement. I have included the code from functions.php with a link to pastebin and was wondering if anyone could take a look. Hopefully, it’s just piece of code in the wrong place.

Code at pastebin