Windows Boot up Issue

I built my rig in Feb. 2015 and haven't had any problems. I know I have a different board than you guys, but it should work the same being the same chipset. I just have more crap on my board that I don't need or use. :)
@KevinUK, could you do as @Kbird suggested and go into bios and set optimized defaults (F5)? While you are in there could you go into the monitor section and give me the readings for CPU Temp, MB Temp and the +12V, +5V and +3.3V? Also, have you had a BSOD on your board? If you don't mind, please run the BSOD Posting Instructions and post the zip file here? Even if you haven't had a BSOD it can give us a lot of info about your OS such as drivers and such. Maybe we will see something that doesn't look right.

Also, could you go to control panel, Uninstall a program and give us a list of your installed programs to look at?

If I ask you to do anything you have already done, please excuse me. I have scanned over the whole thread, but I may have missed a few things.

If you will open an administrative command prompt and run fsutil behavior query disabledeletenotify it will tell you about Trim. If it says

NTFS DisableDeleteNotify = 1 (Windows TRIM commands are disabled)
NTFS DisableDeleteNotify = 0 (Windows TRIM commands are enabled)

That will mean that windows is sending trim commands to the SSD Controller. Yes, Windows should do that automatically, but it never hurts to check.

I'm glad you have verified that trim is working. With my recommended command prompt I said that the results will show that the OS is sending trim commands to the SSD Controller. The rest is up to the SSD. With Kbird's suggested program it verifies that the controller is doing it's job. So, it seems all is well on that front.

Earlier in the thread I saw where it was suggested you run sfc /scannow and you received errors. Did you run it 3 times with reboots in between each time? I don't see where you answered that. The repairs are actually carried out during a reboot. Sometimes it can't repair all errors at the same time, or some repairs can't be done until other errors are fixed first. So, 3 times is recommended.

Failing a clean sfc, did you run from an elevated command prompt
Dism /Online /Cleanup-Image /StartComponentCleanup
Then run
Dism /Online /Cleanup-Image /RestoreHealth
They will appear to be doing nothing but will give you a successful or failure report eventually. If you get a failure report, please let us know the error.

Assuming you get a successful report, run sfc /scannow again.

Also I noticed you were running BIOS version 3301. That is for the new Broadwell chips. For the chips we are running the latest bios is 2101. I would suggest flashing the bios back to 2101 as Kbird suggested. I don't see where you responded to that recommendation.

A weak PSU could cause the problems you are experiencing. Not a diagnosis, but a possibility. Could you go into BIOS and on the monitoring section of BIOS tell us the MB Temps, CPU Temps, the values of the +12V, +5V and +3.3V please. While in bios, I would suggest to set optimized defaults (F5).

If I was having your problems, I would disconnect all hard drives except the OS drive. Also disconnect everything connected to the computer except mouse, keyboard and monitor. I would also use a USB mouse and keyboard and remove any wireless USB dongles or devices. If you have SD cards or USB drives, remove all of them. In other words, I would remove everything from the system not necessary for the computer to run. Test and see if the problem persists.

The BSOD Posting instructions I asked about will give us a lot of info about your system even though you aren't experiencing BSOD issues. Also a list of programs you have installed could help. You can get those easily from Control Panel > Uninstall a program, or if you have CCleaner installed, go to tools then in the bottom right click save to text file.

I know you guys have had issues with your motherboards, but I am not convinced it is a MB issue. The Motherboard is Posting correctly, as I understand it. Once it passes post, everything is handed off to the OS. When you see the spinning circles, that is when the OS is beginning to boot and load drivers. That seems to be the point where you are having your main problem. These are just some of my thoughts, observations and opinions.

OK, thanks Kevin. Those were just some of my suggestions. FWIW, and I admit to being somewhat OCD, even on a clean install I always run the DISM and sfc /scannow on them just to be assured that everything is right and set up correctly.