3 computers now where chkdsk was automatically started

Over the past two weeks I have been seeing some weird behavior on my home computers.

First my primary computer started to act up (slow boots, freezing, and auto-start of windows recovery services, etc., some issues found running dism and chkdsk that wouldn't fix). It seemed the hard drive was going bad, so I bought a SSD. I installed a clean version of Win7 Pro x64. Reloaded everything over the weekend. Everything seemed to be working well. Last night I ran the windows backup (backed up image of C: to drive D:. The program said it finished but this morning there is a warning (the taskbar "notification flag") that said the process failed and I should run "chkdsk /r". So I am running it now on drive D: and it seems to be taking for ever. It's now on step 4 of 5 (it is at 10% on file 76 of 13,xxx). It's taking a few minutes just to go from file 50 to 76. Hopefully it will be finished when I get home tonight.

Then my second (media server) computer went into an automatic "chkdsk" mode the other day. It scanned the hard drive (made a fix I think) and all seems okay.

This morning my third computer (wife's) was acting up. First it was very slow starting/browsing internet, then the computer froze (ctrl+alt+del won't work). When I restarted it up, the automatic Chkdsk scan started. Its at about 22% now.

Coincidence?
I an running Microsoft Security Essentials and Malwarebytes Premium. Nothing was reported by either.

Hi Milesahead,
I did a clean install on the first computer (I did Not restore a backup image).
All the computers are networked together.
All computers are on their own APC battery backups.
I'll watch everything for a couple of days - hopefully this is just coincidence and not a virus of some sort.
As I mentioned, all computers have anti-virus and malware protection.

Thanks for responding.

I now have another computer that is acting up. I went to start my HTPC last night and got a message that boot manager (or such) can't be found "insert disk and hit any key" message. I put in the Windows 7 installation disk but it wanted a Recovery (or maybe it was Repair) disk, which I didn't have. I went to another computer to make one, however when I came back and restarted the HTPC it booted up normally. I am going to run chdsk and sfc fist chance I get.

It may be just coincidental but I seem to be having a lot of computer problems lately.

My wife's computer and my office computer are now rebuilt (clean Windows install) and working fine. The HTPC computer has no data to backup (it just streams video from server to TV) so it would not be a problem to reinstall Win if I have too.

But want is going on with these machines? I am now running Malwarebytes premium (was not before) and MS Security Essentials (which I have always had installed) on all my computers.

Thanks again. I'll head over to Kaspersky now and get this TDSSkiller program. I see that Malwarebytes has a (beta) Anti-RootKit available now at their website. I'll get that too.

MBAM has an option to scan for rootkits that you need to check (default is unchecked). Try that one too.

Thanks.
I installed Malwarebytes premium on the two computers where I just re-installed Windows (so it possible any rootkits are gone with the clean install). I ran the scan yesterday, but not the rootkit scan (thanks for pointing out that scan is not on by default).

I think the Malwarebytes license allows me to install it on up to 3 computer (I'll recheck that) as I have five computers in the house. But I could run the Trial version on the other two if needed.