When I perform the command make install, the include directory has UnitTest++ created twice:
/usr/local/include/UnitTest++/UnitTest++/

I was using the default configuration, but the same happens when I use a different directory on --includedir configure's parameter. In order to solve the problem I edited the file Makefile.in removing the UnitTest++ from the line 496:
pkgincludedir = $(includedir)/UnitTest++/
So now the line is:
pkgincludedir = $(includedir)/

Now the command make install creates the right include path. I did this change because the variable nobase_pkgincludeHEADERS already has the UnitTest++ included in its files path. Maybe that is the cause of the repeated directory in the include path.

Has anyone experienced the same problem?

Thanks.