There are some issues with custom block regions which have been identified. The problems encountered so far are when using Aardvark-Postit Version: 2012071202(DRAG-N-DROP), Aerie and Rocket themes.
After blocks have been successfully created and then moved to the new block-region areas, using AJAX Drag-n-Drop, the page layout no longer appears to work. This behaviour seems to be connected to body classes generated by the dock.js.
The only way to be sure of all the problems is to create a theme that is as simple as possible only introducing 2 custom block regions (4 block regions in total) and enabling the dock.