Did you fix this? everything works for me 95% of the time, but sometimes i'll have a 16x16 swap tiles where part of it won't swap properly kinda of like your example, and if I remap the 4 tiles to be 8x8 swapped then they work.
I can't figure out why it sometimes does this. All my unique tiles are unique. (also 4.1.3)
edit: Just wanted to update, that I moved the 16x16 tiles into another scene, where theyre the only swap tiles, and it worked normally.
I slowly added more swap tiles to the scene and it broke the 16x16 swap tiles again.
I just started using the replace tile within gbstudio, I just like the plug in a lot more and its faster. :(