First, the ppid is 1 so we get nothing useful there. Second, the path is the java command-line (which makes sense) however the launcher for JabRef is 'wrapped' in a launcher script. So we cant easily figure out that that command-line matches that launcher! Thus there is no match and I get 2 icons (the launcher, and a 'default' window icon).
Just to comment on why we cant match Java apps, take a look at this one (JabRef):
rdyer 31165 1 23 23:33 pts/0 00:00:04 /usr/lib/ jvm/java- 6-openjdk/ bin/java -classpath :/usr/share/ java/jabref. jar:/usr/ share/java/ antlr.jar: /usr/share/ java/antlr3. jar:/usr/ share/java/ looks.jar: /usr/share/ java/forms. jar:/usr/ share/java/ spin.jar: /usr/share/ java/glazedlist s.jar:/ usr/share/ java/microba. jar:/usr/ share/java/ pdfbox. jar:/usr/ share/java/ jempbox. jar net.sf. jabref. JabRefMain
First, the ppid is 1 so we get nothing useful there. Second, the path is the java command-line (which makes sense) however the launcher for JabRef is 'wrapped' in a launcher script. So we cant easily figure out that that command-line matches that launcher! Thus there is no match and I get 2 icons (the launcher, and a 'default' window icon).