STM32 Timer Encoder mode delayed by 400ms
I am using two quadrature encoders through the STM32F411CEU6 timer encoder mode. Here is the graph for one of their CNT values:

As you can see, it takes about 400ms to update the value, but when it does, it seems accurate. How can I make it so that it doesn't do this? Timer settings (the same for both):

The PLL is at 98 MHz and it says the peripheral clocks are at 48 MHz, although I'm not sure if that's the right number to read. I've tried changing:
- Encoder Mode
- Input Filter
- Some values of the Trigger Output Parameters, although not all of them
I am positive that the encoders are hooked up correctly and I took a look with the oscilloscope and the signal looks good. I'm simply plotting htim3.Instance->CNT to make this chart.
