Boot Manager fails to find OS loader after running Windows update far I've caught it doing this twice.

Noteworthy Specs:

Windows 7 Home Premium 64 bit
Gigabyte GA-785GMT-USB3
Samsung Spinpoint F3 HD103SJ 1TB 7200 RPM 32MB

*The mobo is always slow detecting the SATA drives from some reason.

Problem: Windows critical updates and wants to reboot. Upon restart ACPI or whatever says it's scanning for storage devices...after a long while it finds the non-boot partition and my external hard drive but not my boot partition. So it gets to "loading operating system" and never does anything. A quick cntrl, alt, delete restarts again and it boots up just fine.

What could be causing this problem? Mind you this has ONLY happened when windows puts out updates. I have not seen it do it with having to restart for any other reason.
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