Is this what you were talking about?
Microsoft Windows [Version 6.0.6001]
Copyright (c) 2006 Microsoft Corporation. All rights reserved.
C:\Users\#@%> sfc/scannow
Beginning system scan. This process will take some time.
Beginning verification phase of system scan.
Verification 100% complete.
Windows Resource Protection found corrupt files but was unable to fix some of th
em.
Details are included in the CBS.Log windir\Logs\CBS\CBS.log. For example
C:\Windows\Logs\CBS\CBS.log
Here's the info from the CBS.log
2008-11-09 17:16:40, Info CSI 0000015f [SR] Beginning Verify and Repair transaction
2008-11-09 17:16:40, Info CSI 00000160 [SR] Cannot repair member file [l:20{10}]"conime.exe" of Microsoft-Windows-ConsoleIME, Version = 6.0.6001.18000, pA = PROCESSOR_ARCHITECTURE_INTEL (0), Culture neutral, VersionScope = 1 nonSxS, PublicKeyToken = {l:8 b:31bf3856ad364e35}, Type neutral, TypeName neutral, PublicKey neutral in the store, file is missing
2008-11-09 17:16:40, Info CSI 00000161 [SR] Cannot repair member file [l:20{10}]"conime.exe" of Microsoft-Windows-ConsoleIME, Version = 6.0.6001.18000, pA = PROCESSOR_ARCHITECTURE_INTEL (0), Culture neutral, VersionScope = 1 nonSxS, PublicKeyToken = {l:8 b:31bf3856ad364e35}, Type neutral, TypeName neutral, PublicKey neutral in the store, file is missing
2008-11-09 17:16:40, Info CSI 00000162 [SR] Could not reproject corrupted file [ml:520{260},l:46{23}]"\??\C:\Windows\System32"\[l:20{10}]"conime.exe"; source file in store is also corrupted
2008-11-09 17:16:40, Info CSI 00000163 Repair results created:
POQ 66 starts:
POQ 66 ends.
2008-11-09 17:16:40, Info CSI 00000164 [SR] Repair complete
2008-11-09 17:16:40, Info CSI 00000165 [SR] Committing transaction
2008-11-09 17:16:40, Info CSI 00000166 Creating NT transaction (seq 1), objectname [6]"(null)"
2008-11-09 17:16:40, Info CSI 00000167 Created NT transaction (seq 1) result 0x00000000, handle @0x144c
2008-11-09 17:16:40, Info CSI 00000168@2008/11/9:23:16:40.417 CSI perf trace:
CSIPERF:TXCOMMIT;4
2008-11-09 17:16:40, Info CSI 00000169 [SR] Verify and Repair Transaction completed. All files and registry keys listed in this transaction have been successfully repaired
I don't understand the last part; it's saying everything has been repaired successfuly...
But, this doesn't explain why Windows doesn't behave normally, yet Linux does. Also, I haven't heard any wierd noises from my HDD or anything. Could it simply be an NTFS problem?
Also, this program had to be run from the command prompt, not the run menu (Win+R).