Version: Heidi 32-bit, 9.4.0.5135 on Windows XP and 5125 on Windows 7
Steps to reproduce: connect to MySQL, add and save a new user@localhost in User manager, then Tools->Flush->Privileges;
Expected behavior: I'd expect to see the 'Flush privileges' command in the log panel, and the newly created user to be able to log into the server (with another client or via the commandline shell).
Actual behavior: only a '/ Ping server /' statement appears in the log panel and the new user is unable to log in. If next I send manually a 'Flush privileges' query from the Query tab the command shows in the log panel and the new user can log in as expected.
Note: the same appears to be true for all commands in the Tools->Flush menu.