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If permissions are set incorrectly you will see a screen similar to the following during installation. Each file and folder with the wrong permissions can be seen with "Not Writeable" writtn in red.
To fix the permissions you can either use your FTP program (click here for file and folder permissions) or click the link shown as Click Here to set permissions automatically via FTP in the above screen. If you click the link you will see a screen like this:
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Enter the FTP Username and password and click Submit. The script will update all file permissions and if successful you will see a screen similar to the following before it returns to the File Structure check screen.
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After this the screen will either automatically return you to the file structure check screen or you may need to use the back button in your browser to return to the Licenses check screen (don't forget to re click the checkbox for agreeing to the license).