When i use the latest phpMyAdmin 2.5.0 together with MySQL 4.1.0-alpha and php 4.3.2-RC2 i got the responce that the authentication failed, and that the main cause was that php used the old client library. 

Mysql says on their page about how to upgrade from 3.23.x to 4.x: 
---- Text from mysql pages ----
Ensure that you don't have any MySQL clients that uses shared libraries (like the Perl DBD-mysql). If you have, you should recompile them as structures used in `libmysqlclient.so' have changed. The same applies for Python MySQLdb.

Upgrading to 4.0 MySQL may not be possible if you run PHP, Perl or MyODBC.... At this time, most rpm's and packages have a dependency on libmysqlclient.so.10, instead of libmysqlclient.so or libmysqlclient.so.12. This does not occur in every case since the linkage process differs with different build strategies.
---- End of text from mysql pages ----

Any chance of precomiled binaries for windows that includes the new mysql lib?? Or perhaps a second mysql module where functions are named mysql4_xxxxx insted of mysql_xxxxx ??