When I do the first step in your response I get a message that it was not able to repair some of the items and it created a log file. It is a pretty large file so I have copied the last part of it that seems to have the error part of the log. Let me know if I should go on to your second suggestion or not.
POQ 66 ends.
2009-11-28 11:54:28, Info CSI 00000167 [SR] Verify complete
2009-11-28 11:54:28, Info CSI 00000168 [SR] Repairing 1 components
2009-11-28 11:54:28, Info CSI 00000169 [SR] Beginning Verify and Repair transaction
2009-11-28 11:54:28, Info CSI 0000016a Hashes for file member \SystemRoot\WinSxS\x86_microsoft-windows-autochk_31bf3856ad364e35_6.0.6000.16386_none_dfbd2b4dc4d6121b\autochk.exe do not match actual file [l:22{11}]"autochk.exe" :
Found: {l:32 b:vdXwQjfUWVuCapX/CYCaZNAfpYa8cFju/xMiM6VoxfA=} Expected: {l:32 b:wSKkBQ/YXr4909/sTSrtOCsbCRFN0hw8v/ecE99qI6U=}
2009-11-28 11:54:28, Info CSI 0000016b [SR] Cannot repair member file [l:22{11}]"autochk.exe" of Microsoft-Windows-Autochk, Version = 6.0.6000.16386, pA = PROCESSOR_ARCHITECTURE_INTEL (0), Culture neutral, VersionScope = 1 nonSxS, PublicKeyToken = {l:8 b:31bf3856ad364e35}, Type neutral, TypeName neutral, PublicKey neutral in the store, hash mismatch
2009-11-28 11:54:28, Info CSI 0000016c Hashes for file member \SystemRoot\WinSxS\x86_microsoft-windows-autochk_31bf3856ad364e35_6.0.6000.16386_none_dfbd2b4dc4d6121b\autochk.exe do not match actual file [l:22{11}]"autochk.exe" :
Found: {l:32 b:vdXwQjfUWVuCapX/CYCaZNAfpYa8cFju/xMiM6VoxfA=} Expected: {l:32 b:wSKkBQ/YXr4909/sTSrtOCsbCRFN0hw8v/ecE99qI6U=}
2009-11-28 11:54:28, Info CSI 0000016d [SR] Cannot repair member file [l:22{11}]"autochk.exe" of Microsoft-Windows-Autochk, Version = 6.0.6000.16386, pA = PROCESSOR_ARCHITECTURE_INTEL (0), Culture neutral, VersionScope = 1 nonSxS, PublicKeyToken = {l:8 b:31bf3856ad364e35}, Type neutral, TypeName neutral, PublicKey neutral in the store, hash mismatch
2009-11-28 11:54:28, Info CSI 0000016e [SR] This component was referenced by [ml:38{19},l:36{18}]"Windows Foundation"
2009-11-28 11:54:28, Info CSI 0000016f Hashes for file member \??\C:\Windows\System32\autochk.exe do not match actual file [l:22{11}]"autochk.exe" :
Found: {l:32 b:vdXwQjfUWVuCapX/CYCaZNAfpYa8cFju/xMiM6VoxfA=} Expected: {l:32 b:wSKkBQ/YXr4909/sTSrtOCsbCRFN0hw8v/ecE99qI6U=}
2009-11-28 11:54:28, Info CSI 00000170 Hashes for file member \SystemRoot\WinSxS\x86_microsoft-windows-autochk_31bf3856ad364e35_6.0.6000.16386_none_dfbd2b4dc4d6121b\autochk.exe do not match actual file [l:22{11}]"autochk.exe" :
Found: {l:32 b:vdXwQjfUWVuCapX/CYCaZNAfpYa8cFju/xMiM6VoxfA=} Expected: {l:32 b:wSKkBQ/YXr4909/sTSrtOCsbCRFN0hw8v/ecE99qI6U=}
2009-11-28 11:54:28, Info CSI 00000171 [SR] Could not reproject corrupted file [ml:520{260},l:46{23}]"\??\C:\Windows\System32"\[l:22{11}]"autochk.exe"; source file in store is also corrupted
2009-11-28 11:54:28, Info CSI 00000172 Repair results created:
POQ 67 starts:
POQ 67 ends.
2009-11-28 11:54:28, Info CSI 00000173 [SR] Repair complete
2009-11-28 11:54:28, Info CSI 00000174 [SR] Committing transaction
2009-11-28 11:54:28, Info CSI 00000175 Creating NT transaction (seq 1), objectname [6]"(null)"
2009-11-28 11:54:28, Info CSI 00000176 Created NT transaction (seq 1) result 0x00000000, handle @0x3f4
2009-11-28 11:54:28, Info CSI 00000177@2009/11/28:17:54:28.896 CSI perf trace:
CSIPERF:TXCOMMIT;6
2009-11-28 11:54:28, Info CSI 00000178 [SR] Verify and Repair Transaction completed. All files and registry keys listed in this transaction have been successfully repaired