When middle-clicking links, why does my browser sometimes open two tabs?

Have you tried using a different mouse? If there is another mouse readily available, connect it and see if the issue persists.

When I've experienced this issue it has tended to be the mouse. Either a faulty sensor or click mechanism that sends two reports in quick succession. Thankfully mice are cheap and easy to test and replace.

If I understand your question correctly, you have this issue with both Chrome and Internet Explorer, right?

If I were to try to cast a wide net to hunt for a ghost bug like that, I would also run a scan against spyware or viruses (AdAware, SpyBot, Microsoft Security Essentials ...)

Is your mouse plugged into a USB port, or does it plug in to one of the PS/2 ports of a desktop PC?

In the latter case, I would try to exchange the keyboard and the mouse plug. If the bug vanishes, you probably have a hardware problem with your first PS/2 port.