I am running 12.04 64-bit and am dual booting with Win7, for full disclosure, although I suspect that has nothing to do with my problem.

Occasionally the boot-loader(GRUB) will fail to load and I will be presented with a black screen with a single blinking line. There is no apparent pattern although I suspect there is one and it is related to a program I am running. This has happened to me eight out of ten power cycles now and I can fix it consistently, however, I have no idea why it happens.

My current fix is to boot a live CD (I've tried both KNOPPIX and Ubuntu with the same result) and that's it. Somehow booting with the live CD is enough to "wake-up" my hard drive. I then reboot and GRUB magically appears again.

So what is going on? Is it possible that a program is corrupting my MBR and the live CD is restoring it? How can I narrow down the possibilities? Thanks.

Additional:

This is still a problem. I'm convinced now that it is not hardware related as I've spent the last month and several boot cycles on Windows without a hiccup. Recently when I started using Ubuntu again the problem started again.

I am more interested in figuring out what is going on rather than actually fixing the problem. Are there any tools, logs, etc. I can use to unravel this mystery?