Weird problems with .exe files on discs (such as games and apps) on Vista Ultimate 64

(I posted this somewhere else but came here seeing as this part of the forum is the one with the most viewers).

Hi everyone, I wasn't sure where else to put this, if it's in the wrong section please if there's any mod out there you can change it to where it might belong to.

Anyway, the issue I'm having is one of the strangest I've seen on an OS.
I all of a sudden had a problem with a certain game and a certain mod which I wanted un-installed but the only way to un=install it is to actually re-install the game.

So I went backed up my files and un-installed my game and then inserted the original game disc in the drive to re=install it.

Now a lot of weird things happen, it just takes too long for the autorun.exe to actually "run", so I go to Computer and check if the disc gets recognized, but the whole "Computer" window is blank...I just eject the disc tray and the whole window comes alive again.

So I try again with another game (also tried this with an anti-virus CD) and something similar happens except this time the whole window freezes and then tells me Explorer is not responding, so I choose to close it (since it's supposed to re-open again automatically) but even though it re-opens it's frozen.

I then had to shut down the PC by holding the power button, turned it on again and then windows loads but takes longer than usual and my wallpaper is missing (black screen) so I eject the disc again and everything is dandy. I put it in again and it takes forever for the autorun.exe to actually run and when it's about to a window asking me what to do (if I want to open the folder on explorer or I want to run "install.exe") and I choose to run Install.exe, which never works and again freezes explorer, I again eject the disc and it doesn't work.

I then restarted the PC and tried 2 different boot discs, one a Vista disc and another Linux live disc...they both work perfectly, also when Windows booted I tried discs that don't have any executables in them such as data discs, audio cds, movie/video DVDs and all of them work perfectly so it's not the drive.

I then tried a lot of other discs that have "exe" files on them and none of them work and show weird behaviour, games, applications etc...it seems Vista doesn't want or doens't know how to open an executable that's in a disc!

I have never seen this before so I kinda doubt anybody has had this problem, I also checked for Viruses and nothing...not even spyware or trojans or anything and I also went to my linux partition and all this discs get perfectly recognized as Windows software (as usual) and nothing's wrong with them or the drive at all it seems.

I can't install my game or anything at this moment that is on a disc (I also tried exploring and sometimes explorer tells me it's a blank disc! or otherwise it shows me the exectuable which I can't execute!).

If anybody can help with this rather odd problem I would appreciate it quite a lot! but I'm afraid I might have to re-install the whole thing, I just hope it let's me backup my stuff!
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EDIT:
I re-installed the OS but the same thing, though now pretty much every other "autorun" disc works but 2 of my games won't work.

Stranglehold (which I bought 2 days ago) both discs (dual layers) and a backup copy of Grand Theft Auto: San Andreas, they both look new (San Andreas isn't dual layer, I thought the drive would probably have problems with dual layers but that doesn't seem to be the case), it's very strange and specially because I tried them under Linux and the drive starts spinning instantly just like with every other disc.

I really don't get this and I've never seen this before, I bought this drive only 6 months ago because the original one of this PC died after 2 and half years of use, but this one is still new and has worked perfectly all this time...it's a Samsung too, the problem is that I bought it OEM so I don't really know if I'm entitled to a warranty...then again, I'm sure it's not the drive but it's specifcally these 3 discs it just doesn't want to read properly and when I click on the executables the "Computer" window freezes for like ten minutes or so, then it comes back and around 2 minutes later it tells me the .exe files are not a Win32 application!!!

It reminds me of when I tried executing older 16bit installers in Vista or XP!!!, it also takes forever to "explore" the discs, I really need help if anybody else knows something please!!!

EDIT #2: Oh and by "read properly" I mean the OS, Vista (which is my theory) but since I've never seen this before at all I don't know what to do and I really want to play my games.