Great question! I had never noticed this point before. At the beginning of the tale, when the narrator receives his sentence, the voices are described as follows:
After that, the sound of the Inquisitorial voices seemed merged into one dreamy, indeterminate hum. It conveyed to my soul the idea of revolution - perhaps from its association in fancy with the burr of a mill wheel.
Of course, as you correctly point out, voices are referred to again in the last paragraph, but under very different circumstances:
There was a discordant hum of human voices! There was a loud blast as of many trumpets! There was a harsh grating as of a thousand thunders!
It appears that the voices in both cases refer to the forces of the Inquisition. At the beginning, note how they all merge into one, "dreamy, indeterminate hum" reflecting the state of the narrator but also the way that the Inquisition are able to decide on his sentence at their leisure. At the end, however, with the invasion force, they are all set apart and divided, thus explaining the "discordant" hum that clearly reflects the agitation in the Inquisition.