'Windows failed to start' message on boot, but nothing to repair?

I have an intermitant problem where I get 'Windows failed to start' with the options 1.Start windows normally 2.Launch system repair.
If I select 1. It will run for well over an hour and give a 'cannot repair message' after which it boots normally anyway. If I select 2. It boots fine with no issues.
Now this might seem like a non problem i.e. just select 2. then, but I am not the only one who uses the machine.
I have tried SFC/scannow, which doesn't seem to find anything, I've tried chkdsk etc. with no joy. There also doesn't seem to be anything in the system event logs that gives me a clue, although I admit I'm not hugely familiar with event viewer and where I should be looking, but nothing seems to be leaping out at me.
This seems to happen maybe twice or three times a month on a machine which is used daily, so finding the solution has been tricky.

Specs, i5 2500k@4.4Ghz 8gb Ram 750w Antec PSU, 2x nvidia 460 in SLI, MSI P67A-GD53 mobo. Win 7 bit Home Edition.

Thanks, I've pretty much eliminated malware as a culprit. Machine is clean as a whistle, and it runs fine. It's just the weird niggle that comes up 2-3 times a month on boot and I am frustrated that I can't nail it down.

Test your hardware starting with HD, and then work through the rest of the Troubleshooting Steps for Windows 7.

Report back as you go as other steps may be indicated.

Thanks, I have a new theory. Is it possible that a power issue on startup could cause Windows not to boot? My house electrics are OK but not ideal. I also have a lot of gear running off a two wall plugs, at least 5 devices using power strips, and sometimes more.
Btw all steps above I have either already done many times over, or have come out fine. The only thing I haven't done is a complete reinstall. I have too much on at the moment and too many installations of various software to want to have to do the dance without compelling evidence that my install is the issue.

May well take a try at that, I don't think it could do any harm i suppose. At the very least if I do it and the problem reoccurs (like I said it's very infrequent) I'll know for sure we have a hardware issue. Cheers.

Where are the results requested for each of the Troubleshooting Steps for Windows 7? If you have questions about performing any of the steps then just ask back. But if you don't do the work, you won't get it fixed.

Compare your install with the perfect install in Clean Reinstall - Factory OEM Windows 7
which compiles what works best in tens of thousands of installs we've helped with here. That's how I'd decide if you need a new install or not. How close does yours come to that install?

Aha, I took another look at the trouble shooting steps, which I had pretty much performed myself. I kinda ignored step one as well as I regularly run CrystalDisk info and keep an eye on failed sectors etc. However I ran Seatools short DST which it failed. Trying to backup now, and I'm sure I'll be doing some drive shopping over the next couple of days.
Thanks for the help to everyone who contributed to the thread
DawnRazor

Time and again the step which is skipped is the one which provides the solution. It literally results in thousands of wasted hours for all of us. Nevertheless we remain the top tech forum in web history because we never give up.