Timing circuit with op amps and capacitors
The output of the comparator is supposed to transition from -13V to
  12V where Vcc is +-15V.


You may easily have damaged your LEDs. When the comparator is supposedly not driving a LED you will have generated -13V to ground across it (and its series resistor).

Most LEDs have a maximum reverse voltage of about 5V. It doesn't matter that there is a series resistor - it's the volts across the LED in reverse that damage them.

Try replacing the LEDs and putting a diode across each one to protect it from reverse voltages. If you have a data sheet try reading the absolute maximum ratings.