Sorry to here that my friend. Lets have another look. Can I presume you haven't use and third party clean up/defrag programs as we discussed?.
How many drives/partitions do you have system protection enabled for.Can you post a screenshot.
Firstly run the system file checker to search for any corrupt system files - SFC /SCANNOW Command - System File Checker
be sure to run from an administrative command prompt.
Check that the following services are enabled in services - Volume Shadow Copy - Windows back-up, and appear like mine below.
Just while we look at this give system restore the maximum amount of space possible by sliding the slider as far right as you can.
Create a TEST restore point and re-boot again.Post back with the results.
Also as a pre-caution you could run a full antivirus scan followed by a full malware scan using Malwarebytes - http://www.malwarebytes.org/