I have been having this issue with KDE 3.2.1 on FC1 2.4.22~2174smp where certain applinks that I create on the desktop open with a duplicate window; or more accurately, a duplicate taskbar indicator with the hourglass. It takes about 20-30 seconds for this second indicator to clear. During the 20-30 seconds, the actual app window's behavior is irregular. For instance, Adobe Acrobat 5.08 will take a long time to respond to an 'open file' request, and Frozen-Bubble will display 'jerky' rendering of marble shots - until the second window indicator dissapears - then all is well.
This behavior does not occur with KDE applinks, whether I create them by drag'n'drop from panel menu, or create them freshly with right-click desktop ==> new file, etc.
I have uninstalled KDE 3.2.1 and reinstalled - no help. This also occurred with 3.2.0.
Not bothersome enough for me to need back on my psych meds, but still a pain in the butt.
Any clues? Thanks.