Hi Felski,
You may be correct that it is an RPG Maker issue. I have not been able to reproduce it, but this is the second time I have seen it. Also restarting the game does not seem to help. I've also tried changing the icon to a different one and saving and then restarting the game and that does not work either. I can see the icon fine in my database and everywhere else in the game. It's just wrong on the skill tree. I know I can simply copy and paste the skill and use the pasted skill ID instead and everything will work fine. I don't want to spend too much time on a minor issue like this. It does not happen every time, and seems like once in a blue moon, though I am sure this is caused by some sequence of copy and paste. Also it has only happened to me so far so you should not worry about it at all unless someone else can reproduce it. My fix is easy enough. I do leave my RPG Maker program open for extended periods of time and perhaps that has something to do with the bug.
Thanks for taking a look at it Felski.