Export Tool Leaving Out Content

Anybody have any idea what might be causing my export tool to leave out random comments and some custom post types?

There is a lot of content, 1300 posts, 7 custom post types each with less than 500 posts, 6000 comments, and the xml files is about 12mb.

I’ve missed a few updates and I always download the xml file before doing so just in case the update breaks something, but every time I’ve tried to import the file into a local WordPress installation to make sure everything got downloaded right, different things are imported or left out each time.