It could be a hardware issue of some sort with the hard drive itself or potentially some kind of deep rooted malware. If you copy the files to a different drive, are you able to toggle off the read-only flag and edit the file normally?

No sir, I tried with an external hard drive and the problem continues.

That's most unusual. Wait, you said the disk where windows is doesn't have this problem. What exactly happens to files when you transfer them off of the affected drive? You said you can't toggle the flag off anymore and edit them. What about copies of files?

Something that I thought of initially is some kind of malware. The only ones that can persist through OS reinstall and format are bootkits:
http://support.kaspersky.com/us/vir.....ns/2727#block2

If it's not that then it's likely a hardware issue with said drive. Using something like Crystal Disk Info to read S.M.A.R.T. and see if there are errors on the drive:
http://crystalmark.info/software/Cr.....o/index-e.html

Problem persisting when you downgraded. or was it only in 10. are you making sure not to use the programs folder.

Problem persisted. Actually the SSD (The disk where windows is located doesnt have the read-only problem) is okay, the HDD, where everything else is, has it. So I'm confused.