Why can't I route the same signal to multiple pins on an STM32F407?
The second pin was misconfigured as an input

I was attempting to use pin PA5 as ETR for TIM2. However the ETR and CH1 alternate functions both map to the same pin on TIM2. Further down in my code I had the following:

ocnt.TIM_OCMode             = TIM_OCMode_PWM1;
ocnt.TIM_Pulse              = activeVideoLineStart;
ocnt.TIM_OutputState        = TIM_OutputState_Enable;
ocnt.TIM_OutputNState       = TIM_OutputState_Disable;
ocnt.TIM_OCPolarity         = TIM_OCPolarity_High;
ocnt.TIM_OCIdleState        = TIM_OCIdleState_Reset;
TIM_OC1Init(TIM2, &amp;ocnt);


because I want to interrupt when TIM2->CNT exceeds a certain value.
Because I set output state to Enabled, the pin for TIM2 OC1 (which happens to be the same pin as ETR) was being configured as an output which had the effect of pulling the pin low, and also pin PA0 which was connected to it.

To fix the problem it was enough to change the code to:

ocnt.TIM_OutputState        = TIM_OutputState_Disable;