With both current stable and beta Catalyst drivers, Portal has a one second input lag, on both keyboard and mouse. Switching back to open source ATI drivers, while slower and less pretty, allows for at least a playable game.
Information that may be of use:
Ubuntu 13.04 64 bit
AMD A10 APU
128GB Samsung 840 Pro SSD for root/app installs including Steam.
I have not had an opportunity yet to see if this issue also affects other Source-based games, but I do know that Counter-Strike based on the old HL engine performs great on both stable and beta Catalyst drivers.