The Fatal Error you’ve pasted above says that you’ve run out of memory. What’s probably happening is that you were running pretty close to being out of memory already, and the Commons In A Box theme has fairly hefty Dashboard settings, so it pushed you over the edge. You can try dropping the following into your wp-config.php file, to see if it helps:
define( 'WP_MEMORY_LIMIT', '64M' );
It appears that your current memory limit is 42M, which is pretty low for an installation of BP + WP + a bunch of other plugins. Bumping the limit as I’ve suggested here should work, as long as your host doesn’t have restrictions against this kind of manual adjustment.
You can safely ignore the other notices.
The BuddyPress menu you see is not a bug. In a recent version of BP, the top-level options were moved to Settings > Dashboard, but we add the top-level menu dynamically when a legacy plugin needs it.