I have a Sony C1xD (really neat subnotebook) with a 1024x480 display. After upgrading from Xfree86 3.3.6 to 4.0.1 I have had problems with the display size settings in XF86Config-4.
Even if I only have one Mode (1024x480) specified, the Neomagic chipset reports that the screen is a 1024x768 and uses that setting (found in /var/tmp/XFree86* log file). The xserver starts, but there are some problems with the mouse pointer coming low on the screen if flips over and comes at the top again. Further, I cant the fvmw navigation windown over the logical screens I have because it is probably placed below my physical screen. Any hints? Anders