Would you by any chance be willing to send me a .yy of any sprite before and one after you update and the texture group and fps is reset? I have not been able to replicate the issue on my end.
In regards to the bounding box being a single pixel in the top left corner when set to automatic, I did notice it in the beginning. I'm currently unsure if I have any control over that since it seems that it's something GM decides upon. Have you noticed whether, if left as is, actually compiles to that single pixel bounding box in-game? Worst case it could be calculated within GM Link.