Sounds weird… and I think there is a problem somewhere else.
The FreeRTOS timer code is completely unrelated to EXTI registers.
Are you sure your ISR is not invoked (and cleared the PR1 bit) ?
Starting the scheduler enables interrupts so maybe a pending IRQ kicked in.
Did you define configASSERT and also enable stack overflow checking for development/debugging. I’d strongly recommend to do so since it really helps a lot !
Did you configure the (NVIC) interrupt priorities right ? For Cortex-M MCUs this might be confusing.
I’d recommend to read the FreeRTOS docs regarding RTOS for ARM Cortex-M .
Also e.g. Understanding priority levels of ISR and FreeRTOS APIs - #16 by aggarg contains a good and easy to understand explanation.
BTW which MCU or FreeRTOS port is it and which FreeRTOS version is used ? It’s always good to add this information.