Anyone been able to get stable USB 3.0 ports and working PCIE 3.0 on either of these MB's?
http://www.newegg.com/Product/Product.aspx?Item=N82E16813131801
http://www.compusa.com/applications/SearchTools/item-details.asp?EdpNo=1610186&CatId=7381 

(I've been about as patient as I can be with my Classified, watching EVGA's site for any updates or a new BIOS, but I guess they've moved on.)

I thought I read in another thred and on the internet this was a problem with Intel CHip being made to a early release of spec. Not all Mfg of connecting devices were following the same specifications. 

KenMcC

I thought I read in another thred and on the internet this was a problem with Intel CHip being made to a early release of spec. Not all Mfg of connecting devices were following the same specifications. 

That's probably the cause..., but it doesn't help when I boot up and have to switch USB plugs around because some of the ports have stopped working.  I thought I had it fixed with an update a while ago, but it's popped back up, and I've had to revert to using an external USB hub again.  I also want a board that will run PCIE 3.0.  I know that the Classified is not guaranteed to do that..., that it's only certified for 2.0, but others, perhaps most, seem to be able to get it working.  I bought it, thinking it would run PCIE 3.0. 
 
I'm looking at a big purchase of a couple of higher resolution monitors, (the old, aging eyeballs like 28 inches at least), and most of the people who have gone to other boards say that they have had much more success than they did with the EVGA X79 boards.
 
I've bought many items from EVGA and spent a few thousand dollars with them and have been very happy up until now, but they seem to have dropped the ball on the X79 boards.  If I could get them to exchange the one I've got for one they could guarantee will run USB 3.0 and PCIE 3.0, I'd gladly do it. 

I saw a thread somewhere about someone who had a sabertooth board and was also experiencing this problem

+1,  its a problem with Intel vs the mfg of devices.  Many of the Mfg have updated / modified the firmware / drivers --in or for their products to work with the Intel chps. 

i wonder if the intel brand motherboards suffer from this issue. I'm guessing probably not?

Nope, not an Intel problem from what I have read.  Numerous people here running Asus boards and not one has mentioned any problems.
My Rampage IV Extreme has had zero issues since December.

I think you will find either of those mobo's will work just fine right out of the box. 
There is no problem with the chip for x79, none at all. Problem is with evga's bios, as is well documented in another thread.
My x79 has been rock solid since day one with all features working.  
dam,  Johnny beat me to the punch by seconds... 

Intel has admitted their design  does not always interface with all USB 3.0 mffgs.  Good enough for me. 

doorules

I think you will find either of those mobo's will work just fine right out of the box. 
There is no problem with the chip for x79, none at all. Problem is with evga's bios, as is well documented in another thread.
My x79 has been rock solid since day one with all features working.  
dam,  Johnny beat me to the punch by seconds... 

 
Yeah, these people who want to blame Intel for this amuse me.  They obviously don't run an X79 system (Or TWO) to know the difference in a working product and a NON FUNCTIONAL one.  
 
Honestly now this point is moot.  There are boards out there with zero issues.  There are boards out there with many issues.  You don't have to search far on the interwebs to know which brands you shouldn't purchase.   
 
Edit:  This is my SECOND X79 Classified with USB problems.  The first was RMA'd within 4 days after I received "Surge on Hub Port" and was told it was a hardware issue by EVGA.  Got the second one and I still get the same warning now and then and my ports (2.0 AND 3.0) are a crapshoot each time at boot.  This is just ONE issue with my EVGA X79 board.