I had this problem eons ago.  Clicking on a URL button calls eventually 
calls browse-url-netscape like I want, but doesn't cause it to pop up
a new navigator window.  At that time I used tm, and I had to hack tm
to make it work.  I reported it as a bug and I *thought* my fixes made 
it into tm-7.106 but I could be misremembering.  Anyway, they
definitely didn't make it into the tm shipped with xemacs.  However
today I (finally!) installed pgnus 0.53 and stopped using tm.  Sure
enough, I've got that same problem.  My `fix' was to defadvice
gnus-button-url and gnus-button-embedded-url to honor
browse-url-new-window-p.  I think it would be nice to have that simple 
change made to the source, though.