@mahk I think I see what may be causing the issue. Try removing all equipment from your character and then use CTRL+R on him to dispel any lingering spell effects. Check if the script works then and let me know how it turns out.
@jpersinne the BGII:EE Thief Controlled script is indeed based on my work in aTweaks (I'm the author of that mod).
It seems that some third party editor may have corrupted the timer on your main character's CRE file. In your savegame, Jan is able to hide just fine with the same script assigned. Another possibility would be that the script was active at the exact moment when your character was dual-classed which may cause the same issue.
Yay, was having this problem too when I exported my Kensai/Thief into BG2. That command line fixed it.
I wonder if another possibility is from importing your character through a save game. I didn't have this script active on my character when dual classing, but it was active when BG1 made the "Final Save" which I used to import my BG1 character into BG2
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Also, are you wearing heavy armor by any chance?
Regardless, it worked oddly for me when my party was split up. Otherwise, fine.
@jpersinne the BGII:EE Thief Controlled script is indeed based on my work in aTweaks (I'm the author of that mod).
I wonder if another possibility is from importing your character through a save game. I didn't have this script active on my character when dual classing, but it was active when BG1 made the "Final Save" which I used to import my BG1 character into BG2