I'm using Ubuntu 12.04 but the same problem applies to subsequent Ubuntu releases.I can start Magnifier (version 3.5) from Ubuntu Dash. But the Dash still shows as semi-transparent, thus making it difficult to use Magnifier in that area. Workaround is to Lock the magnifier launcher to Unity's Launcher bar: but it's anothe icon permanently in Unity's Launcher bar which can be a nuisance. What's really needed is for an icon to go into Ubunto's Notification Area: currently this is done by using an indicator for the appropriate app.
I found a workaround that doesn't add another icon permanently in the launcher area. It could be better, but this works well enough for me: I set it up to autorun on login, but to not bring up a window, it just stays in the notification area.
Here's the GUI way to do it:
Alternately, paste these commands into the command line:
sed -i 's/ShowWhenExecuted=1/ShowWhenExecuted=0/' ~/.magnifier.inicp /usr/local/share/applications/vmg.desktop ~/.config/autostart/Note that, until the authors update the binary past version 3.5 for GNU/Linux, they won't have the vmg.desktop file. I added it to 3.7.1, which you can find here: https://sourceforge.net/p/magnifier/feature-requests/_discuss/thread/0dee3949/52c9/attachment/magnifier-linux-3.7.1.tar.gz