I know how important it is to have enough storage for top performance of your device Jason. System update would normally remain on your phone for proper system file access. The numbers outlined in your post certainly do not reflect the total amount of storage used by Miscellaneous files. You indicated that you noticed this storage issues prior to, and after system software updates. It is highly recommended to do a factory reset http://www.verizonwireless.com/support/knowledge-base-99541/ after system software updates to resolve any type of system conflicts from previous to new software update. Please do a factory reset and see if the storage issues gets resolved.
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