And if you refer to SPDIF option under Audio section in preferences window (as already said in BSPeter's sticky post), it's only for
InterVideo AC3 and not for AC3 Filter
If you want to change AC3 Filters options you can (with a movie with ac3 audio) right-click on BSplayer and choose Options -> Filters -> Advanced and then select AC3 from that window.
Alternatively you can set "offline" options by searching for AC3Filter under START -> All Programs