There are some settings you can tweak:Workspace preferences -> C/C++ -> Indexer.
C/C++ General -> Indexer.
C/C++ Build -> Discovery Options
Project properties -> Resource -> Linked resource, path variables tab.
C/C++ General -> Paths and Symbols -> Includes tab, for each(!) language.
The purplish ones are the ones you added in C/C++ Build -> Settings -> Tool settings tab, (Asm Paths, C and C++ Compiler Directories).
Also make good use of clearing the index. In the project explorer, right click on the project, Index -> Rebuild.
I am only using the AVR plugin so far, but not the Arduino plugin
There are also some reports of the CDT plugin being buggy in those areas
The AVR plugin having path problems
"individual settings for build configurations"
plugin messing things up irrecoverably