Oh, I see what's happening. I didn't look at your first screenshots closely.
So you're doing a fadeout so you can do the party change.
SOME commands will run after a transfer. Your Change Opacity, for example. I believe a fadein is another one that will run after a transfer.
The first thing I would try is removing the autorun event that does the fadein, and on each event that does a fadeout, change party, transfer, do a fadein after the transfer. See if that works.
If it doesn't, just change your fadein event from autorun to parallel process, and instead of setting a self switch, do an Erase Event command. The difference is that a self switch is permanent, and remains when you leave the map and return. But an erase event will just get rid of the event while you're on that map, but when you leave and return it will be there again.
Respectively Solution by:
Shaz
Keeper of the Nuts