You probably have too many ExAnimation entries. Taken from the LM help files:
Note: Although there are 0x20 entries allowed, the game usually can't handle that many extra animations. The top of the screen will start to flicker when you've exceeded the limit. In testing a typical level, I was able to get up to about entry 0x12 for animated 16x16 tiles before flickering started to occur. With just palette animations, I was able to use up all except the last entry before any flicker occurred. YMMV.