Is TIM3 running at all, i.e. does TIM3_CNT register change? Are CH1 and CH2 set to input capture in TIM3_CMMR, and so that CH2 inputs from CH1 input pin? Is the TIM3_CH1 input pin set properly in GPIO?- check the related GPIO registers. Measure input signal directly on that pin using oscilloscope.
JW
