I get notification to posts I replied to over a year ago and also some that I have replied to and unsubscribed to a while back but the only notification I get on replies I make since the new sites been running is when I add a second reply saying new reply that I have just made lol totally confusing. Good to read that you have now got your notifications sorted not now, my email server is gmail and never had a problem until the updated site went live.
Yes, we wrote the web application from the scratch. It's because of security issues and emerging new technology which would make us able to upgrade more easily, which the previous system wouldn't allow.
Regarding the issues. We have more then 40 issues in a queue to be done. Some of them are visible some of them are not visible. We sort them by priority, and we are going to fix all of them pretty soon.
Regarding notifications. Settings on how to receive future notifications is available in your profile. Check the solution which is suited for you and let me know if you still have problems with notifications? If so, I'm going to post an issue with exact steps to reproduce.