Here's a conflict I don't think has been reported as yet. When doing the Earth Warrior quest which involves a trip to Shadow's Rest Cavern, it is impossible rescue Janus Aldarin if the mod Better Dungeons is installed. A simple solution to the conflict is a temporary uninstall of Better Dungeons.
Just to be clear, this report is not a request for a patch, although I wouldn't object to one. Including the conflict in the RST ReadMe along with the work-around seems sufficient to me.
This is my second attempt at a play through of RST after running into the Water Warrior problem/bug some months back. Lots of mods have come and gone in my load order since that initial attempt, so I thought I'd have another go at it. So far, so good, and I’ve been enjoying it immensely.