Hi Rob,
There is a setting in QueryTracker that will automatically close queries on the 121st day if no reply is recorded. This feature was added a while back when too many people weren't recording anything when an agent didn't reply. Wishful thinking, I guess.
If you don't want your queries closed automatically, you can turn it off by going to "Settings" and then "System Preferences" then uncheck the box for "Auto Close Old Queries".
This is an AMAZING new feature I didn't even know about!