Originally you could modify and then update all modules at once, but a default suhosin installation would truncate the POSTed data for many modules + many blocks scenarios.
Based on my testing with 9.3, it appears it's still the case that the default Suhosin configuration will cause problems with the block manager. I believe the solution documented in the Wiki still has to be applied (I didn't think to check if the scaling factor is still accurate though, I forget where that number came from... there was a pretty good reason... it's probably still right), although with the more modest editing scope the size of the limits can be lower. The Suhosin defaults appear to be way too low for this application, however.
I'm still puttering around with the issue that submitting changes to block configuration doesn't appear to work with IE, but does with Firefox. I'm not a very good AJAX mechanic, so I haven't made much progress. I did confirm it wasn't a Suhosin issue (although it was, at first). I fixed my php.ini config when I realized I'd forgotten to make that edit when I migrated the server - and I was the one who wrote the wiki entry!
It is pitch black. You are likely to be eaten by a grue.
Server specs (Server OS / Apache / MySQL / PHP / DragonflyCMS):
Ubuntu 12.04, Atom D525/Apache 2.2.22/MySQL 5.5.38/PHP 5.3.10/Dragonfly 184.108.40.206 CVS