Hi all,
I, and from the looks of it, a number of other 7.x users are having a problem with blocks disappearing in custom-defined regions in our themes. In my case, I created a home page template, with a number of custom regions. The blocks used by these regions include a number of custom blocks using views and widgets, and the pre-packaged 'Recent Content' block.
Every morning, when I go to check on my site, the block assignments for those regions are gone and I have to reassign them. They remain in their assigned regions throughout the day, and late into the night. Then, when I look at the site first thing in the morning, they're gone and I have to reassign them. This only happens with my custom regions, and does not impact any others.
I built my theme off of the Zen theme, and added the custom regions to the .info file for both the Zen and custom theme. These regions also consistently display in the Blocks assignment page, even when the assignments to them are cancelled out. One theory I had is that it might have to do with my caching settings, as I am still in the development stage I had not starting caching my theme, and had it rebuilt every time the page refreshed. However, after doing so, this problem continues.