Safari's search bar overlaps website

The top of Safari (where the search bar, all the tabs and so on is) is overlapping the webpage I'm on. This sometimes goes over the website's header.
Here is a picture of the problem on Apple's website:
This is particularly annoying for websites with search bars like Facebook and Youtube...
How do I fix this issue?

Go step by step and test.
1. Empty Caches
    Safari > Preference > Advanced
    Checkmark the box for "Show Develop menu in menu bar".
    Develop menu will appear in the Safari menu bar.
    Click Develop and select "Empty Caches" from the dropdown.
2. Delete Cookies
    Safari > Preferences > Privacy > Cookies and other website data:
    Click “Remove All Website Data”.
3. Safari > Preferences > Extensions
    Turn off Extensions if any and launch Safari again to test.
    Turn on those one by one and test.

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    Updated Prebinding
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    Initialize HardDrive with complete reinstallation of OSX 10.3.9
    To Summarize Possible Solution
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    Any comments/feedbacks are extremely welcome.
    Hope It Helps!
    iMac G4 800Mhz SD 10.3.9 & PowerBook G4 15" 1 Ghz 10.3.9    
    iMac G4 800Mhz SD    
    iMac G4 800Mhz SD    
    iMac G4 800Mhz SD    
    iMac G4 800Mhz SD    
    iMac G4 800Mhz SD    

    Hello tr:
    Welcome to Apple discussions and thank you for your very very thorough post.
    Your instincts to delete anything named "Norton" were right on the mark. Norton software is POISON to Macs running OS X. An additional software firewall is, IMHO, completely unnecessary. Turn on the built-in firewall in OS X - it is robust. In fact, if it is already on, there may be a conflict.
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