Find your sqlite3 gemspec file. One example is /usr/local/share/gem/specifications/sqlite3-1.3.7.gemspec
Windows:
C:\Ruby21\lib\ruby\gems\2.1.0\specifications
.
You should adjust according with your Rubygem path and sqlite3 version.
Edit the file above and look for the following line
s.require_paths=["lib"]
change it to
s.require_paths= ["lib/sqlite3_native"]