Version: (using KDE KDE 3.5.7) Installed from: SuSE RPMs Start computer & KDE, go to desktop 3, click on akregator systray icon, the main window is shown, but you are at desktop 1.
I cannot reporduce this issue in the KDE SC 4.9.3. That is, when Akregator is hidden in the system try, it always opens on the current virtual dekstop. It does take you to the activity where it was lauched from, but I think that is the expected behavior for activities, and to request the ability to change that you should open a feature request (wishlist) instead of a bug report.