Well, the new version is even more broken than the previous one because it's hanging now! And it still doesn't complete all the notes properly.
Having said that, there is a solution to the problem you are having in both the prior and current versions:
After the bar fills up, press stop and start again. NoteCaddy will process more notes. When it fills up again, press stop and start again. It may take a good 4 or 5 times before it finally completes for real, but after that it works properly.
Please revert to the prior version! You can click start/stop repeatedly to get it to work, but the new version just outright hangs.
Something is wrong with the loop that grabs hands and submits them to the hand processor threads. It is incorrectly stopping before it finishes getting all the hands. (Race condition between your hand fetcher thread and your processing threads? Need a memory fence around some variable keeping track of what hand you're on? Off by one error? Somehow the fetcher isn't finishing the job, but the program still knows not all the hands have been processed! Weird.) Whatever you changed, it's now hanging sometimes when retrieving new hands. Please revert the version right away!