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Do you actually have problems, or just see the message and want it to go away?
Did you mess with /boot/System.map? In my distros it's usually a symlink to a longer named System.map file, like System.map-ide-2.4.18 would be the full name. So maybe it is a symlink and is now pointing to nothing, or the wrong file, or something similar to that.
Type 'ls -l /boot' in a terminal to see if it is a symlink, and what it's pointing to if it is. Find out if the file exists.
If you are still having problems, or my instructions aren't clear, you can post the output of 'ls -l /boot' here to see if anyone can help.
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