Two passwords can be set in a PDF file: the Master (author/editor) password which grants all access to do whatever you wish with the document, and the User/Open (read-only) password which only allows you to view the document along with whatever other permissions the author has granted in the file's security settings. I tried Googling for more info on PDF Passwords, but all I found were dozens of sites and programs all promising to disable/remove/crack PDF passwords. :^/
Have you tried uploading a file without any Master password and only an Open password (which you'd need to provide in the stamping URL)? The Stamper will add a randomized Master password anyway. Sometimes trying various password combinations will stumble into one that just happens to work for your particular file -- e.g., no Master at all, or same Master and Open password, or different Master and Open passwords, etc.
Although we tested the Stamper with a variety of files before offering it as a feature, in real-world practice since then, we have found that some files will retain their original Open password when stamped whereas others simply will not, and we have been unable to identify any clear reason nor even any clues to explain the difference. If we knew why the stamping or password retention failed whenever it does, or any specific difference between files that work vs. those that don't, then we could probably fix it, but we don't, so we can't.
Files created or modified with Mac Preview (or anything else using Mac OS X's built-in PDF libraries) seem more prevalent in reports that the original Open password was not retained in stamped copies or that the file could not be stamped at all; using Adobe Acrobat Pro to create/edit the original file seems most conducive for the best results, although we have received a few reports of problems with files reportedly saved in that program as well (though it's not clear if Acrobat was used to author the file originally or if any other program was involved in authoring or editing the file at any point).
Unlike our standard download process where every buyer receives an identical copy of your original file (passwords and all), the PDF Stamping process creates an entirely new file from scratch for each buyer, extracting only the content from the original file to use in each new, stamped file. This means none of the original file's security settings can simply be "carried over", since we're not merely modifying the original file. When the stamped file is created, any security settings must also be applied from scratch, which is why we provide for copy-paste and printing restrictions in the stamping URL.
Personally, if selling eBooks were my own livelihood, I'd be pleased just to get the Stamper working, and I wouldn't even have bothered with a read-only password in the first place, since that only degrades the customer experience for the buyer without any practical benefit whatsoever for me, the seller.