Since the update, the Filter blocks attached to the pumps are no longer filtering the pollution. As a result getting some nice dark pollution clouds around my pumps as they are concentrating it in a small area.

Thanks for letting me know, I've tested myself and it does indeed seem that the filters aren't being used at all. Looks like it might be a bug in Pollution Of The Realms but I should be able to work around it.

Raised the issue with the author of the mod:
https://minecraft.curseforge.com/projects/pollution-of-the-realms/issues/27

Seems there's a deeper issue here with the way I interact with the filters... am trying to confirm with the author on this.

If you are trying to get rid of carbon, you have to upgrade your filters (using anvil and leaves) to cope with it.

After some testing to confirm it works correctly, what EnderLanky says is correct.
@Golrith make sure you upgrade your filter with both leaves and paper to filter all pollutants and it will work just as before.