The new position isn't a bug
The really nice notification bubble (official name "notify-osd") everybody got used to underwent a design change decision in Ubuntu's newest version 9.10 "Karmic Koala". In version 9.04 "Jaunty Jackalope " it used to look like this:
One of the first things you really notice after installing Karmic is, that the notification bubble is displayed much lower. The interesting thing is, that a lot of people think that this is a bug, though it was a decision to make it look like this. The given reason you can find e.g. here(link) is, that people were complaining about the behaviour in Jaunty, that the notification was blocking the firefox search bar (!!!). If you follow the discussion through the linked thread, the best reason to change it back to Jaunty style definitely is, that you shouldn't change something system-wide because it creates a slight problem with one program. What you also often read is, that it doesn't look like a new feature, rather a bug or at least 'it just doesn't look good'.
Change it back
Unfortunately the design change doesn't come with the option to choose between the Jaunty and the Karmic design, what is a bad thing in my eyes. If you start changing things like this you shouldn't just change it with no option for the user to choose or configure it, via gconf you'd have a decent way to do this.
At the moment the only thing you can do is to install a package with the old design:
1. Download the alternative notify-osd from this repository page:
Julien Lavergne's modified packages page (PPA)
Click on "notify-osd" to expand it, and download a .deb package matching your ubuntu architecture:
something like notify-osd_0.9.24-0ubuntu2~gilir1_i386.deb if you have the standard ubuntu version or
something like notify-osd_0.9.24-0ubuntu2~gilir1_amd64.deb if you chose for the 64bit version.
Just download the correct version to your desktop for now.
2. Install the package
Open up a Terminal and cahnge to your desktop directory, so something like
start the installation by entering
sudo dpkg -i notify-osd_0.9.24-0ubuntu2~gilir1_i386.de (standard ubuntu)
(remember that if you are in the right directory, you just have to type in "sudo dpkg -i" and start typing the package file, eg. not than hit the TAB key to autocomplete it)
3. Logout and Login again to make notify-osd restart and do something to check it out (connection to a wireless, getting a pidgin message etc.)
3a) A cooler way to test it and understand how the notification works in general:
- In the Terminal install a little package with the command:
sudo apt-get install notify-send
- after the installation completed type e.g.
notify-send "Hello World" "This is a test"
and watch ;)