I have been struggling with this for the past few weeks!! I haven't been able to do simple multiple selects in Ubuntu, where you hold the CTRL key while pressing the mouse button. This was very annoying, as I wasn't able to select multiple items in my email program (Thunderbird), multiple files in my file manager (Nautilus and Dolpin), etc.
Simple solution… I am using Compiz for my GUI management in Ubuntu. Compiz provides several options for enhancing your GUI, and provides ways to manual set mouse and keyboard bindings to control the various Compiz GUI tools. I had "accidentally" set one of the active tools to use the binding of "CTRL + Mouse Button 1" for one of the enhancements. It took me a while to find it, as I had to go through each active tool's menu to read all the mouse bindings.Once I found it, I simply changed it to a different mouse binding (e.g. ALT+Button1 instead of CTRL+button1) and viola — multiple select now works everywhere!
While Compiz does check for existing mouse and keyboard bindings from other Compiz tools, it doesn't seem to do the same with the operating system. That is, it doesn't check existing bindings and warn of any conflicts with the parent operating system, like Ubuntu 
It also doesn't check with conflicts from other Ubuntu applications as well. I might go and add this to the feature request list on the Compiz website, to get Compiz to check all mouse and keyboard bindings from the operating system and other applications, and to warn of potential conflicts.
[..] A little unrelated, but I rather liked this website post [..]