Normally when KAlarm is minimised into the system tray, running another instance shows a main window. However, when KAlarm was run using 'kalarm --tray', a main window is not displayed. If the system tray icon is inaccessible, this means that it's impossible to display a main window without killing KAlarm first.
This was due to differences in how unique applications are handled under KDE Frameworks 5 as compared to KDE 4. Fixed in commit c5897d0eabf515a82a62429a726819cb60e255ae (16.12 branch).