Why configure files don't find /usr/local based headers?

[Yuri]

I noticed many times that configure files of various projects fail to 
find headers of third party packages under /usr/local/include.
They run command line like this:
gcc -c conftest.c
and it doesn't find them without -I/usr/local/include.

Is something misconfigured on my system? How to make this issue go away 
without modifying all configure files?

Yuri