Windows 7: Startup Crash

Have an Intel quad core chip
Asus Striker Extreme Board
2x Nvidia 9600 graphics cards
3 HD Drives 1x70 system disc only has programs and windows. All data stored on 2x 500 GB drives running raid
8 GB Ram
Windows 7 64 Ultimate



Machine worked fine with no problems up to 3 days ago. Turned it off and 2 hours later needed to use it again. Windows would not complete the start up. Ran repair but it could not fix the problem. Would not run in safe mode or any mode.Did clean install and all worked fine. Reinstalled a mirror of system and all worked fine everything was back. Windows then ran some updates and when finished closed down. When I restarted it same problem, Windows would not start. I installed the mirror again but Windows would not start so I clean installed again and it runs OK. Anyway to get it to run when the mirror is put back I need the programs?