I have an X99 Classified and an XP941 happily booting Windows 7. My install went in off a USB with Windows 7 Ultimate SP1

I went back and rebuilt my system to make sure of the steps. At a high level, the steps are to make an ISO image of the installation DVD, use Rufus to make a bootable USB drive, enable the M.2 in the BIOS and boot override to the USB drive.

I think the trouble people are having relates to advanced format disk support.

One thing I was able to verify was that the procedure I followed will not work with a Windows 7 installation disk - it must be a Windows 7 SP1 installation disk. When making the image with Rufus, use these parameters:

"Partition Scheme" - Set this to "MBR Partition Scheme for BIOS or UEFI Computers".
"File System" - Set this to "NTFS".
"Cluster Size" - Set this to 4096 bytes.

With this, the USB drive will boot nicely and launch the installation process (I was sure to use a USB 2.0 connection). When I booted for installation, I made sure there were no regular disks connected. I don't know if this is required, but that is what I did.

As for the installation process, just run through and take the defaults, including on the disk partitioning. Once you get a desktop, install all the drivers on then x99 CD and go from there.

vaxman65
I went back and rebuilt my system to make sure of the steps. At a high level, the steps are to make an ISO image of the installation DVD, use Rufus to make a bootable USB drive, enable the M.2 in the BIOS and boot override to the USB drive.

I think the trouble people are having relates to advanced format disk support.

One thing I was able to verify was that the procedure I followed will not work with a Windows 7 installation disk - it must be a Windows 7 SP1 installation disk. When making the image with Rufus, use these parameters:

"Partition Scheme" - Set this to "MBR Partition Scheme for BIOS or UEFI Computers".
"File System" - Set this to "NTFS".
"Cluster Size" - Set this to 4096 bytes.

With this, the USB drive will boot nicely and launch the installation process (I was sure to use a USB 2.0 connection). When I booted for installation, I made sure there were no regular disks connected. I don't know if this is required, but that is what I did.

As for the installation process, just run through and take the defaults, including on the disk partitioning. Once you get a desktop, install all the drivers on then x99 CD and go from there.

 
Yeah, I had tried all that.  A matter of fact, I had reformatted the USB I believe 3 times, twice with rufus and once via windows command w/ the Wins 7 DVD as an ISO.  Not sure if its the SP1 version though and not sure if "Cluster size" on auto also was the same setting you had.  I know I had left it on auto every time.
 
Regardless, it worked flawless with the installation of Windows 8 DVD without doing anything extra.

the beeps are normal, there is a built in speaker on the board.  You can disable it in the bios, along with turning off the LED's on the board as well.  I think its labeled as quiet boot.  Your board is fine, on most other boards you actually have to install the speaker which most people don't, so your board is OK!!