In what mode is the process being applied.. Singularity, though Fx Favorites or in a chainer? If it is being applied through a chainer, is the chainer on the timeline or though 'Apply plug-in chain' in the Fx Favorites menu. Click and crackle removal is sometimes not very audible, so try a extreme setting to confirm it is .. or is not working. The residual output mode should indicate a working condition as well.
You have already confirmed the process or chainer are not bypassed?