Windows 7: Strange startup issue.

Windows didnt start properly after restart? Only time I have seen this before is when it would either reboot in the middle of trying to load windows or if it locked up when trying to load windows. I get this message sometimes when I restart that says windows failed to load correctly and It gives me two options so I always boot normally. Whats strange is it never looked like windows ever failed to start? Also my AHCI on my gigabyte controller isnt working on the EP45-UD3P. Thx for any help!