This is something I've done a bunch o' times before, but ain't working now:
I sent two identical one second layers from FCP to Motion. In Motion I created a garbage mask on the top layer added an animated blur to the bottom layer. The blurred layer does not appear when playing the timeline. Not does a desaturate effect or any effect added to the bottom layer.
FYI, I deleted the bottom layer and duplicated it within Motion with the same result.