In the Galileo version of Eclipse, which is supplied with Quartus® II version 10.1sp1 and earlier there have been issues reported with the indexing of C and C files. These issues can be resolved by changing the indexer to completely parse the source files.
In Eclipse, select Window-> Preferences, and under the C/C option tree, select Indexer. In the "Select Indexer" pulldown, select the "Full C/C Indexer (complete parse)" option.
This issue no longer exists with the Helios Service Release 1 version of Eclipse that is supplied with Quartus II version 11.0 and later.