So, I sent a bug report to CT's BugBox System.
There's an color replace error when you save a frame position, and load application position.
Apparently, if you replace a color of one object, then use the save position. restart application, and load application position, the new color that was set to the object after you saved does not get affected. The object retains its original colors before the color gets replaced. I started noticing this when I was experimenting with it in my fan game remake.
Everything else seems fine when you save/load. The only thing wrong is the color replace does not get saved as well. I don't know how much of a priority this is, but it seems like something that should get fixed. Otherwise, ppl would have to find a way around this error with new replaced colors not getting saved properly.
Also, unrelated note, no one can reply to any of my other topics that may have 0 replies? I sure could use the help. But if nothing, I can understand. Just more work than necessary.