1. Pronto does not have an embedded real-time clock as you likely have already surmised and you are resorting to using the displayTime from GUI.
2. Pronto Script does not run while the Pronto is not docked and the screen goes off. The pronto wakes up every 55 seconds or so to only keep wifi active. If you listen closely to the speaker on the back, you'll hear a small 'tick' when this happens.

3. Looks like you did not declare a variable using var for EndPos. i.e.

var EndPos = myTime.indexOf(":");

4. Did you put a try/catch around this script and actually debug it to see if it was causing any errors?