ISR routine is not properly running

[PixelPirate_88]

@hs2

It’s seems to be a Microchip (former Atmel) SAM4-MCU. No FIFO but with an associated DMA called PDC which can be used to setup a FIFO style behavior.

Yes it is.
Note that, the code works perfectly without FreeRTOS. The overun started occuring when I decided to migrate my code to FreeRTOS.