Some project, e.g. CVS uses CPPFLAGS in configure script to detect the right C preprocessor. Missing --sysroot in CPPFLAGS in environment files would cause the cvs project using host cpp instead of the cross-compiler.
Fix commited in http://git.yoctoproject.org/cgit.cgi/poky/commit/?id=97d3ddedcc9b27f0e3e6c3da71029bee2c326684
Verified now CPPFLAGS has --sysroot.