"A Runtime Error has occurred" is displayed when there is a JavaScript error. You might see these errors more often with Pop-Up Blocker enabled because some web pages are trying to communicate with their blocked pop-up window.

To stop seeing these error windows, go to Tools > Internet Options and click the "Advanced" tab. Under "Browsing", check the box for "Disable script debugging".

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You'll still be able to see JavaScript errors by looking at the page status in the lower-left corner of the browser window. When the status is "Error on page", you can click it for more info.