Did you install Windows on a clean, newly formatted drive, or to a drive that had a previous Windows installation still on it?

Do you actually have a Windows folder on both drives?

As a test, you could save a test.txt text file created in Notepad to your Documents folder. See what drive it is on. That drive is likely to be the drive that Windows has started from, unless you moved the location of the User files. You can also check creation dates and/or last access dates for some files.