Win7 seems to not to like to run chkdsk after *any* crashes anymore (at least on my 2 boxes). Booting took longer and longer until I ran it manually. Took a good 15 minutes to fix everything and now it's pretty much back to normal.
Asus P9X79-Deluxe, Intel i7 3930k @ 4.2Ghz, 16gb DDR3-1600 Kingston HyperX Memory, Coolermaster Storm Trooper case, Corsair AX850 psu, Geforce 680 SLI, Corsair Model H100 w/c, Samsung 840 Pro 512gB SSD, Asus Blu-ray Writer 12x, Windows7 Pro x64
MSI GS Series GS60 Ghost-003 Gaming Notebook 15.6", Intel Core i7-4700HQ 2.40GHz (3.2 GHz), 16GB Memory 1TB HDD 128GB SSD, NVIDIA GeForce GTX 860M 2GB, 4.36 lbs., Windows 8.1 Pro