Windows 7 Safely Delete $UPGRADE.~OS and $WINDOWS.~BT in C:\?

How many hard drives do you have ? If more than 1 ssd/hdd was in your pc and you had your documents, etc. on a 2nd drive prior to the 8.1 upgrade, you'll have alot of weird issue's like this. If this is the case, you're better off unplugging the 2nd drive, doing a clean 8 install, followed by running Windows Update until none are found. Then reinstall 8.1 from the Store, re-run Windows Update until none are found. Then get the updates for the Modern app's, open the Store and in the Charms Barr click on App Updates and then Search for Updates. Install any and shut down your pc. Replug in the 2nd hdd and start Windows. Now point Windows to those folders.

Hi! My apologies- I thought I was posting in the Windows 7 forum. Here's my PC:

New build 10 June 2011
"Andrei"

CASE Cooler Master HAF 912 RC-912-KKN1 Mid Tower
MOTHERBOARD ASUS P8P67 Deluxe LGA (P67 B3 Rev)
CPU Intel BX80623I72600K Core i7-2600K Sandy Bridge 3.4GHz (3.8GHz Turbo Boost)
CPU Heat Sink Cooler Master GeminiII S RR-CCH-PBU1-GP 120mm Sleeve
DRAM 2x [8GB (2 x 4GB) 240-Pin DDR3 SDRAM DDR3 1333 (PC3 10600) Desktop Memory Model CT2KIT51264BA1339] for 16GB total
GPU ZOTAC ZT-40503-10L GeForce GTS 450 (Fermi) 1GB 128-bit GDDR5 PCI Express 2.0 x16 HDCP Ready SLI Support Video Card
PSU Cooler Master Silent Pro Gold Series RS800-80GAD3-US 800W
DRIVE0 (O/S) OCZ VTX3MI-25SAT3-120G Vertex 3 MAX IOPS Edition 2.5" 120GB SATA III MLC Internal Solid State Drive (SSD)
DRIVE1 (Data) Hitachi UltraStar A7K2000 0F10452 2TB 7200 RPM 32MB Cache SATA 3.0GB
DRIVE2 (Apps, Programs & Updates, Web site) OCZ VTX3-25SAT3-120G Vertex 3 2.5" 120GB SATA III MLC Internal Solid State Drive (SSD)
DVD Burner (Y Sony Optiarc, Inc. AD-7260S
BLU-RAY Burner (Z Lite-On iHBS212 Firmware 5L09
O/S Microsoft Windows 7 Home Premium 64 bit, Service Pack 1
External Drive WD My Book 3.0 2 TB USB 3.0
Keyboard Rosewill RK-9000 Cherry MX Switch (Blue) Mechanical Keyboard
Monitor NEC LCD2190 UXi LCD 'twist' tech 1600 x 1200 ppi.
Printer Epson Stylus Photo R280

BIOS 1850 (beta) 2011.07.04 update
Chipset Intel® P67 Express Chipset

Did you re-install the programs on your 2nd Vertex 3 after the new install of Windows ? If no, you'll need to reinstall them again. I had the same ssd, until last month when I upgraded to a 256gb. I also have the same Blu-ray burner.