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I can confirm that I've had the same issue as well. I'm trying to make a Sonic-esque game, using the SonicRetro "Sonic Physics Guide" and following the general method the Genesis games used for building levels, including working with a tileset made up of 128x128 sized tiles. I've never worked with this particular size before, and am wanting to build the tileset as I assemble the level, so that I can get an idea for what tiles will be needed and how to organize things. However, once I added in a new pair of tiles to the tileset, it's been impossible for me to update the Room Editor and actually use the tiles I've added.
I actually ended up making an account here to ask about this same exact issue, funny enough. (Could have sworn I used to have an account when I was tinkering with the original GameMaker Studio, but it didn't seem to exist at all.)