I have the exact same problem and I totally feel the pain and frustration!
I went to the genius bar yesterday with regards to this problem and heres what we established.
USB 3.0 Sandisk Card reader with 16gb Extreme Compact Flash works on every single Mac computers except those with USB3.0 capabilities.
Tried with MacBook Pro 2010 with mavericks and it works
Tried with MacBook Pro 2010 with 10.75, 10.8 and it works
Tried with MacBook Pro Retina Display with Mavericks and it fails
Tried with MacBook Air 2013 with Mavericks and fails
The above was tried at home with a Sandisk and a Lexar USB 3.0 on MacBook Pro 2009 with Mavericks and it works fine
But when its on my 2013 Retina MacBook Pro, I face the same problem as you guys.
My grevience is why can't Apple admit that the made a boo boo? Their geniuses aint much of geniuses if they kept asking us to use our own money to buy different card readers and cards to try and trouble shoot for them! Their solution is for me to get a FireWire version or wait inevitably for a patch from Apple.
I am a photographer and the reason why I upgraded to the new RMBP was because of the USB 3.0 function and now it has failed miserably without any solutions unless I spend more money to buy a new firewire card reader (which oh wait... I would need to buy an adaptor from thunderbolt to firewire too because the sleekness of the new RMBP would be compromised and Apple wants to earn more money!) or... If i cant afford those changes, I can choose to wait... and... wait...