In latest release of SmallTime, sound notifications are not activated when SmallTime is minimised(by clicking the arrow in upper left corner of your screen). I will fix this bug this weekend, do some real testing for a week and then release a version 1.0g where this issue will be fixed.
I am sorry for the inconvenience and I hope you did not suffer any damage by setting up countdowns with sound notifications that were not activated. I personaly forgot to take the laundry out and also burned a frozen pizza badly because of this bug. Also almost missed an important appointment.