There are a number of key combinations that cause a ThinkPad to beep at seemingly random times. For example, if you hold down W E and R there's no beep, but if you hold down T Y and U the machine beeps at you (and really has no reason to).
Go to Device Manager and “Show Hidden Devices”. Under “Non-Plug and Play Drivers” you'll see an item named “Beep”. Disable that and the “random beep” disappears. Once done, of course, you can hide the hidden devices again.