Ben
If you don't run into this and some of us do, then there has to be something in the environment that affects it.
The fact that I have not experienced this problem may be because I am not going through a sequence of events in the configurator as you are doing, so the problem could well be there. What I am suggesting is make sure your environment is 100% intact and your BSV is not corrupt before trying to find the problem in AIM
Losing data is a severe problem, maybe you should export your BSV and do a clean install, also dump your DB to a sql file, delete it and re- import
I run on a Windows Server 2008 R2, MySql5.6 , AIM - 3Gb , Tomcat 2.5GB ,Config 1.5GB.
I try keep my memory utilisation at 60 % of the settings. I monitor this from time to time in the windows task manager
Also, monitoring memory usage is a good indicator of your rule behavior, memory usage should maintain a good average usage and flush itself out periodically . If you have configured a rule incorrectly your system could become unstable. Because of the delinquent rule its uses up all available allocated memory space . So being vigilant in this area is a good idea.
BTW, I found version 6 is very unforgiving when it comes to custom html, I had to redo all my forms for this upgrade, So if something suddenly disappears off the form it could be a corrupt form - but deleting data in the DB sounds like something more sinister