DBD::mysql does need to be built against a specific version of MySQL client- or server-libraries. This is something that is determined when you run perl Makefile.PL when building DBD::mysql. You should verify at that stage that you are compiling with the 4.1 client library and header files.

Since you need to make sure that your webservers still use the old DBD::mysql that was compiled against 4.0.2 for your production code, your best bet is probably to install the compiled-with-4.1-client-libraries DBD::mysql in some special location, and then your test scripts will use lib '/path/to/secret/dir'; When you are ready to move to production with 4.1, you'll just reinstall the 4.1 DBD::mysql on top of the old one, and everything will work without a hitch! :)