Hi Chad,
How are you applying the spatial filter? Via the transformer or the writer ? Also have you tried the spatial relator?
I am using it in the spatial filter transformer, we are passing a bounding box through the filter, linked to our online portal. This works fine when we are connecting to the data through FDO connect. We are migrating to Arc SDE and it will not work with the spatial filter, but will work with a clipper. I need both because sometimes we do not want the data clipped.
Thanks,
Chad