Video portions with letterbox effect by using matte black background getting resized sending to compressor

So heres the just...

I have a short 3 minute action sports video. Ive used the letterbox effect on FCP X for every clip. Now, for the parts of the video that have transitions to white or animated "flash" kind of deal, the transition bleeds onto the black bars of the letter box instead of staying inside the bars only. I researched and figured out to correct this to use a black matte background on top of all the other "layers" and using the shape mask effect. So I did just that by making a rectangle covering everything but the bars and then inverted it. Bam! everything looks perfect on final cut. As soon as I send to compressor, even just in the window where it loads the video the exact parts of the video with the black background method I used, it resizes the video so its just a medium sized rectangle in the middle surrounded by black. Anyone know where I went wrong there?

thanks!