I've just found this on one of Ladyada's pages....
There is a small power supply on the board for generating 3.3V @ 250mA. We don't use the 'built in' 3.3v regulator on the Arduino because its only guaranteed up to 50mA and some SD card need a lot of power when writing. This supply is nice and steady, we can use it as an analog reference too! We have two sets of bypass caps to try and keep both 5V and 3.3V supply nice and clean - the 100uF ones are for the low frequency noise and 0.1 for higher frequency
I guess that explains the reason for not using the 3.3v supply from the motherboard.