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When you want to launch a virtual machine in VirtualBox, you must first run VirtualBox and then start the VM. Here is how to create shortcuts to launch virtual machines in VirtualBox without opening the main program window:

For Windows:

1. Right click on the desktop and select New > Shortcut. Click the Browse button and find the “VBoxManage.exe” file located in the directory you installed VirtualBox to (usually: C:\Program Files\innotek VirtualBox\VBoxManage.exe)

2. After the quotation marks enter:
startvm <your virtual machine name>
like so:
"C:\Program Files\innotek VirtualBox\VBoxManage.exe" startvm Ubuntu
Obviously, replace Ubuntu with the name of your virtual machine. Also please note that the virtual machine name is case sensitive! Then click "Finish".

3. Now right click the icon you just created and on the "Shortcut" tab, select for the app to run minimezed:

virtual machine shortcut

For Ubuntu:

1. Right click on your desktop or a panel and select "Create Launcher".

2. In the "Command" field, enter:
VBoxManage startvm <your virtual machine name>
Please note that the virtual machine name is case sensitive!

For instance, my machine's name is Win7 so in the "command" field I enter:
VBoxManage startvm Win7
You can name your icon whatever you want and also you can select an icon for it.

Update: If you use Ubuntu and you are having problems with transparency in VirtualBox, instead of the above command, use this one:
env XLIB_SKIP_ARGB_VISUALS=1 VBoxManage startvm Win7

Again: change Win7 with your virtual machine name. Now everything should be ok.

Credits: blarts | via geekissimo