This is exactly why I like to defrag a windows install and do the partitioning with Gparted instead of doing it as part of the install. I haven't seen this problem before with the Ubuntu/Mint installer. But I have seen it with several RPM distros and the old Debian installer.
It seems to happen when trying to shrink a windows install. I have no idea why. I have never seen a good fix for this. I would love to know if you find some none destructive way to remedy this.
What I have always had to do was wipe the drive and reformat as a single partition in ext2. Then delete the partition and start all over with the partitioning and formating.
Back-up your data first, while you still can.