As Albert and Giu mention, ScriptCase does not install MySQL. In fact, you could install ScriptCase and run it without having MySQL at your computer at all.
ScriptCase can use a number of different different databases which you define as connections in your project. The database connections can be to MySQL on your own computer, or e.g. an Oracle or SQL Server database on another computer. The most bare ScriptCase project could even use a SQLite server less database on your own computer.
As you have installed the MySQL server on your computer, you can of course use that as a connection in your ScriptCase projects. You can also run phpMyAdmin against the same MySQL server. If you experience that changes in your MySQL database does not seem the same in either a ScriptCase project and/or phpMyAdmin, one of them could be connected against another MySQL server, possibly one on another computer unless you have installed MySQL twice on your own computer (not likely and I do not know if one can even do that). Double check the connection parameters for the database connection in both ScriptCase and the phpMyAdmin that you are running, because both can connect locally to databases on your computer as well as remotely to database servers on other computers via a local network or even the Internet.
I have sometimes experienced that applications/projects/database connections have to be reopened in ScriptCase for the database connection to reflect changes made in the MySQL database while a project/application is open in ScriptCase. This could be another reason for the issue that you are experiencing.