Thanks OMC, I've not tried replacing the file yet but thanks for offering up the file. It's strange because any new project I make (or old versions of my current project) display with the usual palette. But the most recent save of my project always uses that weird palette. I never changed any settings and it's still there after restarting. I've gone back to an old backup for now anyway as I didn't lose much, I'm just afraid the file might be corrupted or something so I'm leaving it for now.
On a similar topic, does anyone know why when I select some pixels in MMF2's image editor, making sure to include some transparent area, half of the time it randomly fills the transparent area with either white or black? This is without using any alpha channel data, and ensuring my secondary colour is set to transparent when making the selection, and before pasting it onto a new frame. It doesn't do this all the time, but it does happen quite a bit. It can be frustrating. Anyone else notice this?