Since 2.5x blender has been using CD_MASK_BAREMESH for updating objects since object_handle_update() no longer has access to G.curscreen to calculate the mask from viewports. The problem with this is after an initial calculation, CD_MASK_MTFACE may be required on draw, so it would recalculate the modifier stack multiple times per frame. One case which caused this is armature animated mesh with texface in a dupligroup. Fix this by having customdata_mask member in the scene, this isn't great design but at least fixes the bug and only changes a few files.