So, I just replaced my GTX 760 with a 960 in my media computer. used display driver uninstaller prior to installing card, when finished uninstalling drivers system was shut down. new card was put in, booted up, installed latest drivers shut down the computer, put it in my truck for transport home(I was at work). I got home later this evening, fired up the system, only to get a message saying drive "X"(cannot remember drive letter) needs to be formatted. I go to My Computer, and notice one of my drives isn't showing up. I figure the obvious, while installing the new GPU I dislodged a cable, no biggie. I cracked open the case only to find all connections were secure and fine, however I disconnected and reconnected all Data cables & power cables to be on the safe side. Upon booting the system this time, the HDD indicator activity light goes solid red, and the windows logo will go on a continuous never ending loop. Safe Mode is a no go, it simply stops at AtiPCie.sys and hangs
 
So at this point I disconnect both my HDD's so all that is left is my Intel 80Gb SSD boot drive. I fire up the system, BAM! everything works like a charm, so I power down the system, and reconnect my Hitachi HDD, power up the system, everything is still rock solid! I power down the system and now reconnect my Western Digital HDD, power on the system only to have it go into infinite windows logo loop.  Now cut to the chase! you get the idea! Oh his HDD has failed....well no! Oddly enough I put the Sata type as Native IDE instead of AHCI(was installed on AHCI and never changed) Everything boots up flawlessly(windows installed proper drivers ect, ect). I have tried re-installed chipset & sata/ahci drivers but no avail. System will simply not boot in AHCI mode anymore, after this computers entire life being in AHCI mode. Literally the only thing that was changed was the GPU, no bios changes of any sort. Sure it's nice that the system is fine chugging along in IDE mode, but the sorcery going on behind the scenes is puzzling to me lol & I'd like to figure this out. The only thing I can think of at this point is perhaps a Bios update being needed for my motherboard, which sadly won't happen as the last update was in 2012 which it has. If anyone has any ideas, fire away!! at least for now I have access to all my drives/data in IDE mode not that performance is really any different any, just the thought.
System Basic Specs:
Gigabyte GA-880GM-USB3(AM3+)
FX-6300
GTX 960
Intel X25 80Gb SSD
Hitachi 750GB HDD
Western Digital 750GB(The drive that no longer boots in AHCI mode, since install of GTX 960, windows 7 logo loop)
500Watt Corsair Power Supply

nope, boot order is perfect. AHCI enabled= Starting Windows screen forever, completely solid HDD activity light
IDE Mode= normal operations. Zero issues
P.S. My SSD in this system is the only boot drive. Thanks for quick reply Rj!

Dude you sound like you got the curse lol. Cure Reinstall windows with all your hardware attached first. I know it sounds like a lot but the time and effort it would take if your already triping over every rock on the ground. If you can get a small ssd for the win install. it will take ten mins and your done on a ssd. just an opinion but youll be happy .
make your ssd the only drive and 3.0 the others will fix it fast.

Sajin
Might want to try re-flashing the latest BIOS.

Motherboard currently has latest bios, however I guess it can't hurt to re-flash it. I think before hand I'll try resetting the bios, which I've been to lazy to do as it involves removing the PSU & GPU lol. Been in the IT world for sometime now, and built countless computers for myself and company, yet this is truly a new one to myself for sure And if it means nuke & paving, I refuse as this system was recently formatted already lol, in which case I'll just leave in IDE mode hahahaha. Anyway a Curse perhaps it is, however curses always get cured in movies....  Anyway thanks for the help & input so far fella's. I'll post back later this evening when I can tinker with it.