Hi guys, thank you for the support but unfortunately the bug is not fixed. I updated to the last version (1.0.10) and the amp-pixel tag appeared again. So I removed the pixel tracking code from the footer (Advance Settings > Enter HTML in Footer) and the script disappeared from the header.
This is what I did to check it and maybe it could help you to debug, adding a simple pixel tracking code (like what I mentioned in the first comment) to see if the amp-pixel-latest.js appears again.