X61 - new drive, sata must be set to compatibility - why?

I'm refurbishing an X61 for a new user. It had serious case damage--hinges were broken, so I sent it off to Lenovo and it looks like new. I thought I would also put a Seagate SSHD in it - ST500LM000.
I cloned the old drive to the new one using Acronis TrueImage.
All seemed to go well, except that I had to do a couple of iterations of startup repair when I started the machine with the new drive installed.
However, after that, things went very strange: 1) When I attempted to download any file in IE10 (windows 7 enterprise, fully patched) clicking on the resultant dialog box did nothing--I had to run firefox to download any file. 2) Windows update would not run--the wuauserv service was not running and could not be started. 3) eventually, the machine started giving "non-genuine" warnings.
Since one of the fixes for non-genuine was to do an upgrade install, I tried that--used 64 bit enterprise upgrade windows 7, and it went through what appeared to be the whole install and at the end said: Windows setup cannot configure Windows for this hardware." and rolled back.
Reading about that message led me to discussions about missing RAID drivers, and that got me to try switching between AHCI and Compatibility.
With the bios set to compatibility (2.22) the system works fine--no non-genuine warnings, windows update works, I can download files in any browser I choose.
The system is up to date according to system update 5. I even downloaded the 13 hotfixes for Windows 7 64 bit listed in the download center and applied them one by one to see if SU missed anything. To my surprise, 3 of them DID install, but made no apparent difference to the behavior.
I'm perplexed--This is not a large drive--500 Gigs. I've read messages here about SSDs and large drives in x61, and it seems it should be fine. When set in compatibility mode, the Intel Matrix Storage Manager complains its driver isn't properly installed, but that is the only sign of anything awry.
Performance seems excellent--I think the hard drive number in the Windows Experience Index went from 5.2 to 5.9.
I can certainly leave it set this way, but I'd like to understand why--anybody have a good idea?
Bill Sanderson
Solved!
Go to Solution.

Hi Bill,
That drive is an advanced format drive - 4096 bytes per sector: http://www.seagate.com/files/www-content/product-content/momentus-fam/momentus-xt/laptop-sshd/en-us/...
This can cause a number of issues with pre-SP1 Windows 7 and friends. Even if you're at SP1, there is a matrix storage manager version around that can also cause problems. Your update install was maybe from pre-SP1 media?
A few things to try would be a MS fix (http://support.microsoft.com/kb/982018), rerunning the SP1 update, trying a different Intel storage driver. You may need to do one or all of these things _before_ the clone op.
Z.
The large print: please read the Community Participation Rules before posting. Include as much information as possible: model, machine type, operating system, and a descriptive subject line. Do not include personal information: serial number, telephone number, email address, etc. The fine print: I do not work for, nor do I speak for Lenovo. Unsolicited private messages will be ignored. ... GeezBlog
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