When changing the activity icon, its generic icon (that that is made of those random pieces) covers the user-configured icon. You need to close the Activity manager and reopen it to see your configured icon.
If you use a big icon such as start-here or user-desktop you can clearly see that it is behind the generic icon.
I can confirm. Runing 4:9 Beta 2 currently
Git commit fbe6962a7f9b09525a494b99e2d5ad5a484fd422 by Marco Martin.
Committed on 20/06/2012 at 15:18.
Pushed by mart into branch 'master'.
make sure the right icon is shown
M +1 -0 plasma/desktop/shell/activitymanager/package/contents/ui/ActivityDelegate.qml