Does it fail to recognize a card in that slot in the first place, or only does so with all cards plugged?
Some motherboards disable one PCI-e slot if the adjacent is populated. Or it can be that you forgot to disable sound, firewire or whatever else the MB has that isn't required for mining in the BIOS and is using PCI-e lanes.
Ubuntu isn't usually a very stable or mature Linux distro. May or may not have influence, not sure.
As a side note, I've read that 14.1 drivers give lower hashrate.
Edit: Read the 2nd post here:
https://bitcointalk.org/index.php?topic=296581.0