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For some background you may want to take a look at http://world.episerver.com/Blogs/Magnus-Strale/Dates/2009/12/The-new-initialization-system---How-to-write-an-initialization-module-and-advanced-topics/ and especially the feedback which was entirely correct.
The presence of an IsInitialized property that should not be touched by the initialization module that you write is counter-intuitive. I also saw some internal confusion as to how the IsInitialized property should be handled and we have therefore decided to remove it and move the state handling into the initialization engine instead.
The blog post referred to above will be edited shortly to reflect the changes, which are:
Note that this is a breaking change from EPiServer CMS 6 RC1! At the very least you will need to recompile your code if you have written your own initialization module. It is also highly recommended that you remove the IsInitialized property from your module implementation.