Interestingly, when we isolate the problematic SQL statement and replace its parameters with actual values, it executes in just a few seconds in pgAdmin. However, when we run the same SQL query through our application using Npgsql, it takes over ten minutes to complete.
Another reason could be a poor type casting by your driver/middleware. Can you share the query that is problematic? (also, since you mentioned a version upgrade, also make sure you run ANALYZE; post-upgrade.)