I hit what is a type of Black Box issue. Above the enemy in a fight you get what you will see in the picture. And no it isn't an icon from your sheet. It's hard to explain, but after completely redoing my icon sheet, I got it fixed.
How the issue happened:
I placed my own custom icon sheet in file. (Yes, first place was blank and no black box icon anywhere.)
Yup, I was confused.
How I fixed it:
Deleted mine from the game file, opened gimp and set my grid to 32 x 32 and made sure every single icon was in the right
spot. Deleted the white background from 3 icons I didn't realize had it. Then simply placed it back into the game file and black boxes
are now gone.
Simple:
Not sure what caused it or fixed it, but here is what happened and what I did. Hope this helps.
I can't get the image to load, but here is a link to them.
http://forums.rpgmakerweb.com/index.php?/topic/47195-black-box-over-enemies/
(Note: I fixed my issue without saving an image, this is from another person on here with the same issue and yes I messaged them to let them know I fixed the issue and if there is anything I can do to help let me know.)