Why does it take so long to update the GUI

Scanning chunks and searching inventories is a time consuming operation, so in order to preserve UPS we have to limit the number of chunks we can scan in one tick and the number of inventories we can search in one tick. Especially big saves with a lot of chunks and inventories require a lot of time for indexing & searching. Detailed performance information can be retrieved using the /gh_status command.

For some reason the mod is not updating the ghost/inventory status correctly

Try the command /gh_reset which should force reset the complete mod memory and start from scratch. If this did not help please start a new discussion on the mod page.