What the timer is doing is very funny, I set 15 minutes timer while a song is playing, then I let the song continue for 2 minutes, song is still playing, exited the app and opened chrome and back to Poweramp, checked timer (still counting down) paused music exited Poweramp open Chrome and back to Poweramp, timer was active but not counting, I did not deactivate the timer I pressed play, music was playing I checked the timer, timer have started counting down from 15 minutes previously set.
So what the timer is doing is, if you set the timer, at any given point (timer is active) and you pause the music and exit the app and you reopen the app and press play, the time I will start counting from the previous set time, (15 minutes) and start all over.