I have never used themes so I'm not sure if the above themes are somehow preventing you to stop getting flash on queries and beep on queries. But hopefully we can sort it for you.
1. Options (Alt + O) > IRC > Options (Make sure Query is checked)
2. Options (Alt + O) > Sounds (Make sure Enable sounds is checked and also, select Query from the drop down and make sure it reads Beep on the button below)
Hope that helps and good luck!
