Secure Boot broke my fresh Windows install. What happened?

I reinstalled Windows 7 (x64) on my UEFI supported laptop just fine. Because I was using a USB for setup I had to disable Secure Boot according to the how-to here. USB was prepared as an EUFI device. So Windows works perfectly. Until I decided to check the BIOS and see if Secure Boot was on. It was disabled and I forgot. I Enabled it. BOOM. Windows wont boot. Saying it couldn't read some system file in a EFI Boot dir. I forgot the exact error. Think this action broke my Windows. I disabled Secure Boot again. It still wouldnt let me Boot to Windows. So what now?

And what happened?

Did BIOS say, well Sir your OS does not have secure boot certificates or whatever. So it is illegal and we need to punish you by corrupting your OS?

I set BIOS to failsafe defaults. Still no luck. It still says I need to pop in the Setup DVD and do a system repair. What the hell.

Ok that then makes sense.

But did the BIOS now corrupt my Windows installation in any way because it found I id not have a "valid OS" according to UEFI standards or something?

EDIT: I found CSM has something to do with UEFI and Secure Boot and it was disabled. So I enabled it. Windows 7 is now booting again. But it feels.. whats the right word cause English is not my native.. Tainted?
Did this situation made Windows change some of its components or something?
I thought CSM is only for legacy BIOs. And Windows7 supports UEFI just not Secure Boot. So why the need to enable CSM for W7 to start?

So it seems you need not to let a setup disk repair anything. Just disable Secure Boot and enable CSM.
I gusss if you did install with secBoot you need to set the reverse to Boot properly.

Realy, who the hell came up with that stupid Secure Boot. And for what reason. Security? Microsoft has all the backdoors to your OS anyway. So security was and is never "an issue" for you as a consumer. NSA will breach your OS whenever they want to with MS' help. Its not to protect consumers against malware. That's a big joke. Windows IS one big Trojan horse in your privacy. So it's Secire Boot is stupid and useless. Just takes more of your precious time and energy to figure it out. Nerds....