Instant JChem updated over the weekend as you posted. I was surprised that all of my databases required the tables to be updated. They had done so previously for 5.5.0 so didn't expect that. Took 8-10 hours for 30-40 GB of databases with 3.2 GHz processor running at close to 100% - ie both cores and threads flat out.
Your post today suggests that this shouldn't have happened but wasn't given any choice. Without updating I had message saying schema had broken.
Any thoughts ?