Really this is a variation of a more generic problemof not uninstalling old
obj runtime stuff before installing the new stuff ... picking up the wrong
version is going to be a possible issue whenever you install more than one
runtime on a machine.
That being said, I guess this particular case is more likely than most, and
should be avoidable (as you say) by making sure the compatibility headers
aren't used by the configure process.
I've updated things to try to do that (svn trunk).