Thanks, Ben. I did you first two suggestions and there was no effect as you expected.
We shot Alexa 422 and I use the ProRes 422 (HQ) preset.
Our layering is varied. The problem happens with simple picture overlapping picture with both being Alexa sources. Each subsequent layer make the shift even larger. Those elements can be .tif, .psd, .pict., .tga. It happens with them all. Even when there's just one, it still happens and like I said, every layer creates a bigger bump.