CXX in configure.in, vs CXX as arg to configure: different results

[ted]

I get different results if, on the one hand, I set CXX inside
configure.in, or if, on the other hand, I pass a CXX argument when I
run configure.  The C++ compiler is, in both cases, the one I indicate.
 But what's different is the list of libraries that get placed on the
link line.  (I'm using autoconf as well as automake and libtool.)

I could of course provide more details, but for now my question is one
of principle; should I even expect these two different ways of
specifying CXX to be equivalent?

(In case I've already been too vague: inside configure.in I have
something like this:
case "${host}" in
     *aix*) CXX=mpCC_r
     ...
esac

The other way is to run configure like this:
./configure CXX=mpCC_r 
)