Disable the CTRL+CLICK to follow a link

This may be occuring in Outlook when Word is the email editor, but the setting is in Word. Go to Tools, Options, and on the Edit tab uncheck the box to use Ctrl+Click to follow hyperlink. Make sure that you use Ok buttons to exit out and close Word. This should do it.
HTH

I have never encountered that problem but I guess you could always try either :

1- on the advanced tab of the internet options, uncheck the "reuse windows when launching shortcuts"

2- go in your folder options, file types, find html, advanced and modify the open command by unchecking the "use dde" option

I know you asked about this a year ago, but for the benefit of others, make sure that the Google pop-up blocker and any other pop-up blocker you are using on Internet Explorer is set to allow pop-ups to the site you are trying to connect to.

We use a java applet to launch hyperlinks to various websites and this has been a headache to correct from a support point of view.

It looks like answer 1 is the closest solution to what you are experienceing. If you can provide some details about the application you're experiencing the behavior with, we can get you a solution specific to that app.