Example from unit test:
Project pkg-config-0.25.
Resolving include directive "glib.h" in the file:
/var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/tests/array-test.c.

Include resolver:
baseFile=/var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/tests/array-test.c

System include paths:
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/include
/usr/include

User include paths:
/var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/tests
/var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10

Include resolver wrongly suppose that path 
/var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10
does not exist.

Checking by file system and CndFileUtils.exist() shows following:
File /var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/glib.h exist and CndFileUtils.exist() returns true.

See part of unit test log:

Feb 9, 2011 9:16:49 AM org.netbeans.modules.cnd.apt.support.APTAbstractWalker onInclude
SEVERE: failed to resolve TOKEN{["#include ",<INCLUDE>,line=31,col=1],offset=1189,file=null} INCLUDE{<U> [""glib.h"",<INCLUDE_STRING>,line=31,col=10],offset=1198,file=null}
using resolver:
APTIncludeResolverImpl{
baseFileIncludeDirIndex=0,
baseFile=/var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/tests/array-test.c,
fileSystem=org.netbeans.modules.masterfs.filebasedfs.FileBasedFileSystem,
systemIncludePaths=[org.netbeans.modules.masterfs.filebasedfs.FileBasedFileSystem:/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/include, org.netbeans.modules.masterfs.filebasedfs.FileBasedFileSystem:/usr/include],
userIncludePaths=[org.netbeans.modules.masterfs.filebasedfs.FileBasedFileSystem:/var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/tests, NOT EXISTING org.netbeans.modules.masterfs.filebasedfs.FileBasedFileSystem:/var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10],
fileSearch=APTFileSearch{impl=APTFileSearchImplementationImpl{project=pkg-config-0.25 /var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25}}
}
and cache entry APT cache for /var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/tests/array-test.c
Not resolved path glib.h
Not resolved file glib.h in folder /var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/tests
Not resolved file glib.h in folder /var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/tests
Not resolved file glib.h in folder /var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10
File /var/tmp/hudson0/tester-cnd-test-downloads/pkg-config-0.25/glib-1.2.10/glib.h exist! CndFileUtils.exist()=true
Not resolved file glib.h in folder /usr/lib/gcc/i686-pc-linux-gnu/4.1.2/include
Not resolved file glib.h in folder /usr/include