There is a separate "Timer Volume" on the Pepperplate app settings (under the Timer Alert Sound).
If the timer volume is working correctly, this is a good Apple support note about the mute button:
If your iPad is set to mute - press the iPad home button twice and slide the panel all the way to the left to see the audio controls. The left most button is set to either mute or screen lock.
If you press the mute button there it will toggle mute on / off. After that the timer sounds should work.