That is normal, even in continuous mode, it’ll split clips at 4GB. This is due to the camera using FAT32 as the format type for SD cards. So technically, it’s a limitation of FAT32.
Though, I read somewhere that when GPU (CUDA) is enabled, MRQ is always turned on, even if you don’t check the box. Your identical times via direct export seems to prove that.
Just install the CS6 version, and it should work just fine.
EDIT:
I take that back. Even if Encore CS6 is installed, it doesn’t show up in Dynamic Link like it used to. That definitely needs to be addressed by Adobe.
A couple of other people have had that same problem. Try uninstalling the Blackmagic software, reboot, re-install the software, reboot again, and plug in the device.