It appears the CDT parser does not know the proper paths to properly parse the #include statements in the code. As a result all code that uses information from these includes does not get parsed/marked up properly and are not shown correctly in the source window.
This bug has 2 parts: The first as previously mentioned is that the #include paths to search are not being passed into the parser. And the second is that the CDTParser is not passing back a CodeReader when a #include is encountered.
I have just checked in a new CDTparser.java with a new added method that accesses the API for the ELF header that passes back all of the source files found there. The only include files listed in the ELF header are ones that are actually used in the program itself. If a "#include" line is in a program and nothing from that include file is used, that include file's path is not listed in the ELF header. This also means the source window will not mark it up with highlighting at the present time. I will leave this bug open for now. More info may be forthcoming and after that I will decide whether to close or not.
This has been fixed in CVS head. Now the include paths are added to the DOMSource class as retrieved from the ELF header.