We've dealt with a variety of issues relating to multi-threaded conversions and the root cause always seems to be the same: the users were added through the configuration manager. A bug has been logged with Adobe, so this should be gone by the time ADEP releases later this year.
In the meantime we have a simple workaround: add your users through the adminUI instead (http://help.adobe.com/en_US/livecycle/9.0/adminHelp/admin.htm?content=000159.html)
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