Hmm...In the Command Prompt, type chkntfs /d and press ENTER. (Note that, here the letter D means Default and NOT D: Drive!) Then reboot the PC, ScanDisk should run and check ALL the partitions, let it run, do not cancel it.
After this, reboot again, and check whether E: drive is scanned again or not.
If E: drive is scanned again at bootup, then at the Command Prompt, type
chkntfs /x E: and press ENTER. This should solve the problem.