As you mentioned in your post, hc is creating mySQL databases and PhpBB is working too. Its mean database created by HC in mySQL Server is connected with PhpBB pages. We dnt support PhpNuke & PhpMyAdmin therefore I am not sure about their working.
#1251 - Client does not support authentication protocol requested by server; consider upgrading MySQL client.
If you get this error in HC then you have to follow these steps:
You need to update 2 files of mySQL(libmysql.dll & mysqldump.exe) into hc installation path. Please follow the below instructions to configure mySQL server correctly with HC.
Stop all IIS and HostingController Services.
Copy libmysql.dll from (X:/mySQL installation path/Bin) path of local or remote MySql machine and replace at these locations X:\Program Files\Advanced Communications\Hosting Controller\exes and X:\Program Files\Advanced Communications\Hosting Controller\dll of HC Primary machine.
Copy libmysql.dll from (X:/mySQL installation path/Bin) path of local or remote MySql machine and paste at this path of X:\WINNT and X:\WINNT\System32 Folder HC Primary machine.
Copy mysqldump.exe from (X:/mySQL installation path/Bin) path of local or remote MySql machine and replace at this location X:\Program Files\Advanced Communications\Hosting Controller\exes Start IIS and hostingcontroller services.