The last 2 steps are the problem.
You'd already created the complete dynamic stamp before these steps. When you used the Acrobat stamp tools, i.e. "Custom Stamp > Create", to create a new static stamp, that new static stamp had exactly zero features you'd spent all that time creating. Basically, the tools destroyed all the previous work. So don't do that. Delete anything you created with the Acrobat stamp tool. And by delete, I mean go to the Acrobat stamp folder and delete the files.
So, to fix the stamp. On the 3rd to last step, "I reopen Adobe using a standard PDF". Add a document Title to the Stamp PDF. This will set the stamp category. Now you have a complete stamp. Save the stamp file locally to your project folder, and then copy it to the Acrobat Stamps folder.
Restart Acrobat. Now you will see your new stamp in the stamp list. And if you did it all correctly, the background will be transparent when placed on another PDF.
Thom Parker - Software Developer at PDFScriptingUse the Acrobat JavaScript Reference early and often