Upgrading from 4.0.x to 4.1.x does take a long time sometimes (close to 100 steps for that 1 version). If each step takes 20 seconds (some might take several minutes), then it is possible for it to take 40 minutes for 1 version.
Just in case something is wrong, please check the upgrade log files which are located at internal-data://vw_logs/upgrade on your file system. There we can see which steps it has completed so far and which one it's working on.