For what it's worth, I ran into this problem after upgrading (via a Norton Ghost 11 cloning operation) a 512GB drive in a Thinkpad W500 to a 1TB drive, which (as I came to realize in retrospect) also amounted to upgrading from a 512-byte block size to a 4K ("Advanced Format") block size. Windows Update, Windows Search, Windows Defender, and some other features on my Win7-64bit system were newly failing in various manners after the otherwise unremarkable disk upgrade. Even IE and Flash were showing weird behaviors such as failing to respond to clicks on options in pop-ups such as the Yes/No options in the Set Edition pop-up at cnn.com and the Open/Save/Cancel options after downloading a file in IE. All other methods described on the net for fixing a broken Windows Update failed to help (e.g., running MS Fixit, turning Windows Update auto-run frequency from Auto to Never and then back to Auto, deleting the %windir%\SoftwareDistribution\Logs directory, etc. etc. etc.), but then I found some articles (including MS KB982018) referencing this curious interaction between disk upgrades and Windows Update, and in the end the one and only one thing I needed to do was upgrade my disk driver from the Intel Matrix Storage driver (version 8.9.0.something) originally supplied with my W500 to the latest Intel Rapid Storage Technology driver. First I did a backup and created a restore point just to be safe, then ran the iata_enu.exe file (Intel RST driver package 11.7.0.1013 from December 3, 2012, see https://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&DwnldID=22194&ProdId=2101&lang=eng&OSVersion...) that I had downloaded from Intel's support site, rebooted, and voila, everything began working fine. There was an unusually intense amount of disk activity for about 5-10 minutes after I logged in the first time after the reboot (I'm guessing it was all the previously broken Win7 features "fixing themselves"), such that at times it almost appeared the system had become unresponsive, but after all of that initial disk activity settled down, everything worked fine and all the prior weirdness I had seen following the disk upgrade had resolved.
-- Larry Afrin
Medical University of South Carolina
P.S. In retrospect, I guess I could have also installed the 3/22/13 (12.5.0.1066) or the very latest (5/2/13, 12.6.0.1033) RST package, but hey, 11.7.0.1013 did the trick for me, so unless I find some other bit of goofiness down the road, I'm not sure I see a point in upgrading again.
Moderator Note; s/n edited for member's own protection
