The “timer stays at 00:00” problem
Your system clock shows your local system time. In many cases this time may be different from our server time by a minute or more.
The popup uses the difference between the server time and your local time to manage the counter. If your clock time is different than our server clock time, you may see the popup timer to stay at 00:00 until your local time catches up with the start time of the call as detected by our servers or until call hangup.
In system preferences, you can find your local system time including seconds.
There are servers all over the world whose primary job is to ensure that they know the current time down to the partial second! http://www.pool.ntp.org/en/
Compare your local time with the official time. If there is a difference, you may want to adjust your local time.
You can find the current time here (look on the right hand side): http://www.usno.navy.mil/USNO/time/ntp
or here: http://www.time.gov/
Your computer can synchronize your local system time with these servers automatically for you. This is what it looks like for a Mac user: