I've had the same problem with my (now outdated) Sapphire HD 6790's. Reformatted my system, installed the new 14.4 drivers, and the first thing I noticed after final setup and checking cards, was that one had been disabled. Went into BIOS (Sabertooth 990FX bios 1604), and all looked as it should. After tweeking buses, voltages, clocks, etc, I rebooted, and still no recognition of second card and a message to check Crossfire ribbon. Shut down, pulled ribbon, flipped it the opposite direction (as if that makes a diff, but just in case..), switched power cables from my RaidMax RX 1000AE on the cards, booted again, and finally see the seciond card, but @ 2x, not 16x. Again, I go back to the bios, up voltage on NB, and CPU, raised mem speed to 2000mhz (Crucial Ballistics 2133mhz DDR3) and set timings accordingly. After reboot, I now see the second card @8x. After a few hours of experimenting with voltages, clock speeds, timings, checking Crossfire ribbon, changing power cables, etc, etc, etc, I'm still stuck in card #1 @16x, card #2 @8x. I've yet to uninstall, and re-install Catalyst drivers, as unless there is a serious problem with them, they normally tend to work. As much as I hate to spend time in the mobo bios, uninstalling, re-installing, or switching Catalyst drivers, unless someone has a sure fire cure for this that gets posted pretty quick, that's what I'll be doing in the meantime. My thoughts on this, are that it "seems" to most likely be a bios voltage tweek (at least in my case) issue.
PhenomII X6 1090T/Sabertooth990FX/RaidMax RX1000AE/2X4Gb Crucial Ballistics2133/2Crucial M464Gb SSDraid0/WD-SATA6 Tb/2xSapphireHD6790