When using PCB Team Design (Design Partition) that is how it works, features are deemed separately and will still be deemed when the Global and Shape transparency is set to 100% in the Color Dialog form.
Using PCB Team Design, you have the ability to export a partition of just the Silkscreen layers which means that the SILKSCREEN_TOP & SILKSCREEN_BOTTOM subclasses under PACKAGE GEOMETRY, BOARD GEOMETRY and REFDES will be deemed differently in the master design giving you a visual representation of what has been exported and if you attempt to move these deemed elements you will not be able to because they will be owned by the exported partition until the updated are imported back to the master design.
Not sure if the original user that posted the question ever figured out what was going on, there may of been a database issue causing certain elements to be deemed differently than others. I believe he was sending a request to support to see what is going on.
Hope this helps,