I noticed in the POI Finder thread that since RoK there is now some sort of a eq2ui_custom.xml file that is used to add custom add-ins. As it stands now I had to manually copy that file over from the default UI to get POI Finder to work.
I know it isn't directly related to ThorUI, but it would be nice if the custom UI's kept in sync with the default UI when new (notice I didn't say newer) files are added. I had the same problem recently with the detrimental effects window that they added.
At least that way we would pick up new files not present in the custom UI so there is less of a chance of breaking when new features are added.