Solved ran /scannow and need advice

I have startup issues where I can only run Vista with Selective Startup in msconfig. There are also problems with System Restore so that there are no restore points saved and I cannot create any, getting the "catastrophic..." error. It took work to get it to boot other than in safemode, so I am pretty happy that Vista seems to run fine the way it is. So I decided to run SCANNOW just to see what it says -- I am not savvy about whether it relates in any substantial way to the above issues, but the results show something not right, in the following ways: When I run /SCANNOW it stops at "verification 43% complete. Windows Resource Protection could not perform the requested operation." I take this to mean it never got to the "repair" portion of the operation at all for some reason. When I run /VERIFYONLY it goes to "Verification 100% complete. Windows Resource Protection found integrity violations." Details in CBS.log on C:\. The log is long. Could someone please comment on what this could mean and whether or not it could relate to boot and/or system restore problems? What should I do next? Thanks.

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