I came across this issue posted by Justin Chalfant on Microsoft Connect
https://connect.microsoft.com/ConfigurationManagervnext/Feedback/Details/1834142
You can read his blog post here: http://blogs.technet.com/b/jchalfant/archive/2015/09/29/configuration-manager-2012-sp2-r2-sp1-incorrectly-sizes-partitions-during-formatting-steps.aspx
Basically the Recovery Partition is assigned 1% of the remaining space, when it should be 100%. Here is a screenshot to help you visualize what is happening
Keep in mind this is without MDT Integration, which has its own issues.
David Segura 