Austin.. Since your post has been made for awhile n with no response, I'd like to give my view on using CTM to protect Windows system partition (as most people would do with CTM).
In my case I allocated around 30GB to be my system partition, with a few vital programs such as anti-virus n firewall installed alongside with Windows on it, and kept all other programs/files on other non-system partitions. By doing so my system partition's fragmentation level would stay relatively low over time, and also I will not have the problem you face since all other Big files are not on my protected partition.
Use other forms of back-up for your big files on non-protected drive/partition !