Difficult to answer this without seeing the design or at least the symbols. I'm not sure why this is occuring, but I do have a couple of workarounds.
1. Disconnect the current slots and move them into the desired locations.
2. View_PCB normally assigns slots and reference designators based on the order the parts are placed in the design. Removing the current parts, packaging to reset the internal counters, and then readding the slots in the desired order should also achive the desired effect.
3 Forward to the PCB, gate swap, and then back annotate to the schematic.