Dear Bill and Tim,
thnx for your advice.
No resolution yet but this is what I have done and found so far:
Ran checkdisk again on the OS HDD. Everything seems ok (only 231 unused index entries and corresponding security descriptors that were cleaned).
Did disk cleanup and defragment (was already in good shape because I do it weekly).
Ran memtest86+ and Windows Memory Diagnostics. Everything fine.
Ran SFC again with the same results. It again asked for a restart because some files were in use, I did it, rerun SFC, still the same. Nice eh? I wonder if SFC handles updates and patches efficiently. Besides that Media Center and Time look like working ok. (By the way, I found a bug in Media Center: if you maximise the window in your second screen you cannot take your mouse back to the primary screen). Anyhow this SFC issue looks to me irrelevant to everything else and rather an issue on its own (on my machine for some reasons or W7 related).
Tried the Western Digital tool (Lifeguard) and HDTune Pro on the drives. Tip: latest Lifeguard does not work in W7, use previous version. Lifeguard says everything is ok (SMART and tests). HDTune gives a warning for CRC error count on both drives, but not for my external WDBook and consults to check the cables. Disk surface scan is ok in HDTune also. Interesting point: HDTune gives SMART data for the external WDBook, but Lifeguard not!!
Note: I do not believe that is a HDD or a cable problem. The OS HDD is 4 months old and both cables a week old. Every time HDTune is ran gives the same raw number of CRC errors which indicates that this a tally stored in the drives, and not an online finding.
What I didnot do (and will do in the coming hours):
run a full test in Lifeguard for the sake of it (will take a couple of hours).
install Intel drivers for my chipset (I have left the default W7 ones). I have the disks defined as AHCI.
run a full antivirus scan (athough it scans all the time at idle).
The history of the problem is that I have w7 since Nov2009. Till mid Jan I got a banch of Event 11 (source Atapi, "The driver detected a controller error on \Device\Ide\IdePort2"). I put new SATA cables but still the same. Comes and goes sporadically. Since then i got also Event 11 for CdRom, Event 55 & 57 for NTfs. In the meantime, i got some BSOD's that seemed to damaged the file system which was recovered through standard repair functionality and the w7 installation disk.
I am not an expert but it seems like drivers or hardware.
Please keep on feeding in your input...