I have this problem too.
My hardware is similar (ATI Mobility X1400, Gallium 0.4 on ATI RV515). Firefox is the main app affected (well, it's my most used app too), but I saw this issues with Thunderbird and nautilus. Restarting the respective application helps.
F16 with last updates, I don't have a custom xorg.conf file
$ uname -r
$ rpm -q xorg-x11-drv-ati
I will start to look in the xorg logs with time...