Hmm, it's really weird: I tested again and again (last the daily build 2017-06-06) and duplex printing now seems to work for me as intended - independent of Windows system print settings.
Regarding the margins issue, the changed defaults for me lead to only minimal changed behavior, but no solution (see attached activity_Margins.log):
1. Invoke jEdit with empty settings dir
2. Invoke print dialog first time: margin values are displayed as integers (25), print/preview buttons do work
3. Close print dialog
4. Invoke print dialog next time: margin values are displayed as real numbers (25.0), print/preview buttons don't work
5. Don't close print dialog but change all four margin values: margin values are displayed as integers (25), print/preview buttons do work
6. Repeat as of point 3 ...
In the "Print..." dialog, under the "Appearance" tab, there are radio buttons for "One side", "Tumble", or "Duplex" printing.
When I select duplex printing, the printer properly "prints" both sides of the paper, but the back side is blank. In other words, the front side prints, the printer retracts the page, and the back side prints; but all the text is on the front side only.
Other applications (e.g. acroread) print duplex properly using the lpr flag "-o Duplex=DuplexNoTumble").
How can I find (and fix?) the command jedit uses to print?