Hello Robert. I have done some troubleshooting from my side and I think I have found the problem as it relates to not being able to sign up for updates to threads. I currently have 200 threads marked to send me updates and the only way for me to get notification is to post to a thread. I went to my updates page and deleted the last 50 notifications that I had. After that I attempted to add another watch on a thread and when I went to my notifications screen I could that the new thread had been added. It would appear that when you post to a thread it is removing the last watch automatically. However when you simply click the 'Receive email notifications' button it is not forcing the removal of the last notification. I have tried this 3 times and although some times I still need to click multiple times on the receive notification button I am finally seeing the threads added to my watch list. So it would seem that some of the problem is resolved. Hopefully this will help you in getting to the root cause of the issue.
One of the Jive support engineers has 1892 watches set. They are running a more current version than we are, so that might be the cause, but I'm not sure. I am still working the caching angle (i.e. caching as root cause) as well.