PNG files add colors to the FM file only if they use less than 16 million colors. You won't see this problem if you make sure your PNGs use a 16 million color depth.
You can fix any FM document that suffers from this by either of the following methods: 1) Save the FM as MIF, then open the MIF and save it as FM. or 2) Use the Replace Colors script with FrameScript. --Doug