I run a java program (smartgit for example). What I see in the launcher is just a question mark.
Marking the "Keep in Launcher" doesn't open the app. It just blinks for several seconds and stops blinking (no app is launched).
I even created a launcher file (.desktop) and also did not work.
I followed this but did not help. (Defined StartupWMClass in the launcher file)
It seems that the side bar icon does not even point to the launcher file, because after enabling the Terminal, the terminal is shown when running from the command line or nautilus but not when running from the launcher.
Here is the content of the launcher file (Perhaps this will help):
#!/usr/bin/env xdg-open
[Desktop Entry]
Version=1.0
Type=Application
Terminal=false
Icon[en_US]=/home/alik/Apps/smartgit-2_1_6/bin/smartgit-48.png
Name[en_US]=SmartGit
Exec=/home/alik/Apps/smartgit-2_1_6/bin/smartgit.sh
Name=SmartGit
Icon=/home/alik/Apps/smartgit-2_1_6/bin/smartgit-48.png
#StartupWMClass=sun-awt-X11-XFramePeer
#StartupWMClass=SmartGit