Interesting thread. I was having similar issues with 3000 MHz 15-17-17-35 kit (CMK16GX4M4B3000C15) on both MSI X99 SLI and Asus X99 Sabretooth motherboards. On MSI it was sometimes working and sometimes not, like many people said here, sometimes boots sometimes not. On Sabretooth I was always booting with XMP, but I was getting instant errors with all tests like, AIDA, OCCT or MemTest86. I have tweaked my way out of that somehow, but to this day I cannot boot if those values are set manually, even though identical as XMP, it has to be XMP otherwise I won't boot with anything more than 2400 MHz. This memory really gave me trouble and two nights of tweaking. It turns about that this X99A SLI mobo wasn't bad, it was memory. Although I don't regret returning it and getting Sabretooth, this is amazing mobo.
I still don't quite understand what is going on with the memory. On MSI it wasn't fixable, on Asus basically only setting Fully Manual Mode to Enable helped definitively, even though all the voltages are identical to ones set with this mode disabled.
Anyway, my settings in case someone reads this thread with the same issues on the same mobo:
XMP
Fully Manual Mode - Enabled
VCSAA - 1.178 (1.84 effective)
VCCIN - 1.95 (1.984 max effective)
DRAM - 1.33 (1.356 effective)
Timings 14-16-16-34-2T