Why not call Adobe for paid support? It's work, let them pay.

My thought is the export is changing the pixel count along the way. You didn't reveal the input width and height and the result. If it's not something even such as 640x480 down to 320x240 the software has to select the nearest pixel.

Again, all this should have been covered in your Film School classes but I'm finding folk that didn't go and later they are missing the training or why things work like this.

If this was mine and I wasn't getting the result from the TRANSCODING (that's what this export is doing) I'd use one of my other transcoders to do the work.