are the spatial filters the same?
Is it intersect? within a distance of? within a distance of geodesic? within an extent?
The combination of the filter geometry and the filter method and the coordinate system can yield unexpected results.
If you have an extent defined in geographic coordinates, I would not simply project that extent (either physically or ont he fly) without using a geodesic densify first.
Perhaps so more details would help clarify, given my translation skills are limited.