Using the Eclipse IDE for C/C++ Linux Developers (Version: Indigo Release) with g++ 4.1.2 (on Scientific Linux CERN 5<
It's not Qt per se - it's the CDT Indexer and the Qt Eclipse Integration plugin fighting. I find that performing a clean sometimes 'resets' the includes list in CDT project settings (only does this with Qt integration plugin running), but because Qt uses the .pro file - the compilation succeeds but CDT's CODAN (which uses the Eclipse project settings) throws a fit.
It's intensely irritating, and I haven't found a fix. Also Qt haven't updated the Qt Eclipse Integration for awhile, they want people to use Qt Creator - but it's awful for general development.