Actually mySQL keep changing their API in every new release so some customers will might get this error[ 'Client does not support authentication protocol' ]after upgrade to any supported 4.1.* version. You can follow these steps to fix that issue.
Steps:
1. Stop IIS (with command iisreset.exe -stop)
2. Stop all HC services.
3. Copy libmysql.dll from the /bin directory of mySQL.
4. Replace libmysql.dll in /exes and /dll directory of HC with the dll copied from the mysql install directory.
5. Replace mysqldump.exe in /exes with the exe copied from the mysql install directory.
6. Replace libmysql.dll in C:\WINNT and C:\WINNT\SYSTEM32 with the dll copied from the mysql install directory.
7. Start all HC services
8. Start IIS (with command iisreset.exe -start)