After I installed a Xubuntu-session in addition to my existing Ubuntu-session, eveytime I login to the Ubuntu-session, the notify-bubbles appear with the Xubuntu-theme. Can I revert that somehow?
Have a look at this question: Unity Notifications do not look normal? Removing some Xfce packages (with the "purge" option) worked for me.
If you do need the package
xfce4-notifyd for some reason, you could try to modify OSD configuration as offered here: How to customize on screen notifications?.