Chewy,
In my experience RX is sensitive to adjacent regions/events. I have had the same experience in Pro Tools and it has depended completely on which regions were adjacent and what process I used in RX. Even though I had edited the dialog first and placed crossfades where I wanted them simply denoising or doing some other process would undo those fades and I’d then suffer clicks.
The solution has been to simply bounce/consolidate the regions/events into one file before processing.
My hunch is that this is an Izotope RX problem and not a Nuendo problem.