Responding to your questions in order:
1) If a PDF cannot be stamped for any reason, download links for that file would simply issue an identical copy of the uploaded file, so this would explain why you received an unstamped file with the original User password, indicating the file was not processed through the Stamper at all.
Note that PDF Stamping will not work on a file within the first 15 minutes after you upload that file, so wait at least 15 minutes after upload before you place a test order or use Send Free Download Link to issue yourself a test link.
If the file you upload has both a Master and User passwords which differ, you must specify the Master password in your PDF Stamping URL; this is so the Stamper can fully unlock the file to extract its contents and recompile them into a new PDF that includes the stamp and any other limitations you tell the Stamper to apply. Also, password-locked files can only be unlocked for Stamping if they were saved with the Compatibility option set to "Acrobat 5.0 And Later" (PDF v1.4) or lower, not "Acrobat 6.0 And Later" (PDF v1.5) nor higher.
If this doesn't explain why your file was not stamped, please email support with the proper password to open your file, so we can download a copy and open it to examine its settings more closely:
2) Your uploaded logo looks nice and sharp to me now. Perhaps your browser was showing you a cached copy of the page from before you uploaded the new logo, so it was loading the new logo image, but stretching it to fit the old logo's dimensions. If you're still seeing a distorted logo, try holding Ctrl (on PC) or Shift (on Mac) while clicking the Refresh button, which should force your browser to redownload a fresh copy of the page.
3) That sounds like a known bug in old versions of the Flash player plugin for Mac:
It appears that Adobe has fixed that bug in more recent versions of Flash, so upgrading your Flash plugin should resolve the problem for you:
4) If you don't have your own Web site or don't wish to paste our buttons into your site, you have the option of posting product listings to your own E-junkie Shop page on our site, listing your products at a specific URL where you can send buyers (http://www.e-junkie.com/37 for example, or http://www.e-junkie.com/162913 would be your own Shop page). Items in your E-junkie Shop will also appear in the general E-junkie Marketplace when you have an active paid subscription for E-junkie. This help page explains more about posting product listings to your optional E-junkie Shop:
The Marketplace primarily just provides a way for search engines like Google to find your products, if you don't have a site of your own that they would normally find otherwise, or if you can't or don't wish to paste purchase buttons into your own site. Posting product listings to an E-junkie Shop page isn't necessary, nor very useful, if you primarily sell directly from your own site.
E-junkie Marketplace is not a major shopping destination site like eBay or Amazon; buyers don't really come to our Marketplace and just browse around looking for things to buy. Most sales in Marketplace happen because of search sites like Google sending buyers directly to a specific product page, or because the seller's own advertising and online marketing sent buyers directly to their E-junkie Shop or product page. If you sell from your own site, you would of course want Google and your own advertising sending buyers to your site, so Shop/Marketplace listings would only be a distraction from that.