You have to be careful when using programs such as windows washer, or registry cleaners. Programs such as these clear out cahes and temporary files. Since restore points are only meant to be kept 2-3 months they are considered temporary and removed by these programs.
You may want to try loading a Last known good configuration this is not as reliable as system restore, but any fatal errors on your system should be recovered (if you require to do so).
This can be done (on most systems) by holding the F8 key while your system is starting up, giving you the advanced startup options, and simply select it from the list. Otherwise press what ever key you use to get into safe-mode. As a last resort, you can press and hold the power button during start-up (I do not recommend this) to shut it off, with an incomplete startup, windows should automatically give you this screen on your next power up.
Then create a restore point or 2 and change the settings in any programs that may be deleting them. Even Norton's one button clean up has been known to delete them.
Keep in mind that the system restore is not a save all for data, it simply takes a 'snapshot' of your system's configuration and upon restoring replaces and removes any registry keys, or system files that have been changed or created in since the requested restore point.
If you wish to backup data you should use backup (located under the same menu as system restore) it also has an append option to add to a current backup.