This seems to be a CDT problem. Have you recently updated your version of the eclipse? This topic is discussed in the eclipse forum:
http://www.eclipse.org/forums/index.php/t/216821/
Perhaps this gives you some inspiration on how to get around this problem.
EDIT: As a temporary work, you can disable certain code analysis functions and markers. To do this, go to Window-> Preferences → "C / C ++" → "Code Analysis" and disable some or all of the problems. I disabled everything, since it will still highlight errors detected during compilation, and I will not confuse the falsely declared problems.
Tom
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