in my cPanel page, which is the control panel for my internet hosting, there is a place to go in and administer a mySQL database. Once inside that tool, there is a popup window for entering in SQL queries. At one time this would spawn a popup window. Now it simply loads a new tab within the same browser window.
Assuming you have not blocked popup windows, quit Safari, then go to Home/Library/Preferences and delete the com.apple.Safari.plist file. Then restart Safari and see if the problem continues.
Yes, you do have that file, or Safari could not run. You're looking in the wrong place. Don't look in the root folder, look in your Home folder (the one with the House icon), then go to Library, then Preferences and find that file.