OK, that problem with the signed applet not saving the .POV file should be fixed.
see http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip and also JmolAppletSigned0.jar that you have a link to there. Sorry about that! You were absolutely right -- the difference was that the menu adds a "?" to the beginning of the file name to force a dialog; the command line did not (and was supposed to give the dialog anyway).
>>Bob, now I am really curious about your failure to get anything open at the link to the custom Jmol version on Proteopedia
http://proteopedia.org/wiki/index.php/1stp?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned0.jar . It should be working. I often find the first time I try to load it just by pasting in the address that I do get it hung up on the background even though I answer the questions. However, hitting the reload button then triggers some longer process and after answering the questions again it usually loads correctly. I initially had problems running large structures that way but this isn't a large structure and I imagine you have the Java memory increased above the default? Could it be a PC vs. Mac browser incompatibility?
Java memory has nothing to do with it, I think. I don't know if that page is trying to do some sort of behind the scenes activity during the dialog or what. In any case, my experience is that the first time I get it, then subsequent loads like that -- with the redirected applet -- all I get is background.