IGP motherboards won't work as fast if you let your cpu frequency go down to 1Ghz on AMD machines because it also reduces the memory bandwidth, which can prevent VDPAU from working properly. The cpu frequency governor only relies on cpu usage, it ignores saturation of the memory bandwidth, so it sees no reason to up the frequency to 1.8GHz+ (which has the same memory bandwidth as at full speed). If you are running cpufrequtils, the solution is to add min_freq="1.8GHz" to /etc/conf.d/cpufreq (at least in arch linux). You can also set the minimum speed through /sys/devices/system/cpu/cpu0/cpufreq/scaling_min_freq (at least I think you can). Dual channel memory also helps with the memory bandwidth. IGPs have this issue more than discrete cards as discrete cards generally have very high memory bandwidth by comparison to the cpu->system ram bandwidth. I'm not sure whether the HT multiplier is reduced at 1GHz cpu, or if it's just that having cpu speed the same as HT speed reduces the bandwidth available (though that wouldn't really make much sense to me).
See the bottom of http://apps.sourceforge.net/trac/archvdr/wiki/ArchVDR
for where I got this from