Do you want to check the file and directory permissions on your server match those specified in the post installation instructions in the knowledgebase?
You can run this feature in 2 modes. Check and Update. One shows what would be done if the permissions, which you can set on the screen, are applied and the other shows the changes actually made.
It is possible that your server will throw 500 "Internal Server Error" if you set the permissions to values they do not like. As you get a display of all the changes made, make sure you test your site before you leave the results page. (You can set everything back.)
Sometimes you can get this when you upload files for a contribution.
Being paranoid, I recommend you back up you site content to your pc using an ftp client before playing around with permissions.
Also it would be good if you know how to change permissions from your ISP's control panel and using an ftp client such as filezilla.
Support thread : http://forums.oscommerce.com/index.php?showtopic=311123&hl=