This is what I see in the launcher when I open JDownloader
I don't want to create a launcher that always stay in the dashboard, I only want see the apropiated icon when open JD.
I suggest you report a bug, because this is a common problem with applications that use wrappers to launch.
JDownloader is a java application and uses a wrapper script, so it's going to be difficult to fix this issue, unless Unity is modified so it can track this better.
open a terminal and write this:
add this line at the end of the file:
save it, and launch JDownloader