Do you get any type of message on your screen like 'Windows is now shutting down'?
Do you have Fast Shutdown enabled? I can't really see how installing IE6 would have changed this but you could check.
To enable it do the following
Click Start, point to Programs, point to Accessories, point to System tools, and then click System Information.
On the Tools menu, click System Configuration Utility.
On the General tab, click Advanced.
Click the Disable Fast Shutdown check box to clear it, click OK, and then click OK again.
Click Yes when you are prompted to restart your computer.