when you say "modified configurations", do you mean you added some config files in
/etc/somewhere, or that you compiled the package with different options?
If the former, then those files, if declared as configuration files, should not be touched when upgrading, as per Debian policy: http://www.debian.org/doc/debian-policy/ch-files.html.
If the latter, then well yes, apt-get is doing what you ask: it's entirely upgrading the package (and all its binaries) with a new version. If you want to exclude a package from the upgrade process (rather, if you want to keep a specific version of a package regardless of whether an updated version is available), then you need to "pin" the package. See more about pinning here: