I have assigned shortcuts for some applications via systemsettings->input actions. Some times I notice that if I start the applications immediately during login, it leaves 2 entries in task manager. One wont go away even after quitting it. I noticed this with kmail.

One way to make it go away is to remove the task manger and re add it.

doesn't it go away after a short delay? (e.g. 30 seconds)

if not, congratulations, you found a bug
please report it at bugs.kde.org. thanks!

p.s. the application should be auto started if the session is saved...

It does not go away at all. Even after quitting the application. Only way to remove the ghost entry is remove task manager from panel and re add it.

I have disabled auto saving session.

weird.
please report it at bugs.kde.org, so you're sure developers know about it.