Generally, I don't understand why you are mixing two methods to load Slots:
method 1. With bank select and program change you can load any of the 625 Slots in Performance Mode.
method 2. Why are you using MIDI control changes - that would be CC# 50-54 - to load Slots within the same Performance, if your software has capability 1?
CC# 50-54 are adding the following (intended) complexities. Text passage picked from the Main Manual chapter MIDI:
If Rig Button Morph is activated in System
Settings, and the PROFILER receives subsequent control changes #50-#54
following the initial Slot load, these will trigger Morphing. So, the same
button could be used to first load a Rig, and then act as a Morph Button for
that Rig. To support all functions, values 1-127 should be sent when the button
is hit, and value 0 should follow when the button is released. The setting of
the “Momentary” option in Rig Settings determines whether the Morphing latches
the morph sound and base sound, or if it immediately returns to the base sound
as soon you release the button.
Closing these CC#s 50-54 by sending value 0 - but not too early - might be adding complexity, that you don't seem to need. If you intend to use Morphing, you should use CC#80 instead, which works with any Slot and never loads another Slot.
I also don't understand, why you don't mute sound via a simple CC#7 value 0, which emulates volume pedal in heel position. A dedicated "Mute Performance" is not needed. But perhaps your software sometimes does and you are not aware. The state of volume pedal is global and survives Rig and Slot changes!
I'm wondering, if CC#47 is also involved. This just preloaads another Performance and needs to be followed by one of CC#50-54 to effectively load a Slot. Perhaps the display of the preloaded Performance is irritating. It's not yet loaded.
And if you send MIDI commands related to a Slot which is not enabled, this Slot will intentionally not get loaded.
We have no reports, that one can effectively load any other Slot optically, while acoustically the former Slot remains. And very many people are using MIDI to load Slots.