Have you changed your Shadow Copy Storage ?
If you have reduced this to such a small amount,SR will not retain all restore points,it is just not possible.
Just reading through Google,and a lot is said about Diskeeper deleting restore points,however there is no valid reason why this would happen (not that i could find).
I would suggest you change your shadow storage allocation and create a new restore point immediately-download a small legit program and install this,then reboot the computer and see if SR is working...maybe run DK and see if it still removes SR points.
How to adjust your Shadow Copy Storage allocation click here