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The inability to specify the order in which package-initialize loads packages creates a conflict with some of the user.el files. If some of the user configuration files modify settings in some of the other packages managed with ELPA, errors result when starter-kit tries to run these files prior to package-initialize completing. It would seem like the user files would be a good place to modify packages in ELPA in addition to builtin emacs features. I see this has been encountered in #108 & #107. I'll try to figure out if there is a work around that doesn't involve building a huge init file.
It looks like @technomancy merged this into the code in 2.0.2. However in 2.0.3 in marmalade, the esk-eval-after-init hook has been removed.