More of a heads up than a problem since I have a solution but for any one else using a non NT JQuery script you may encounter this issue.
After upgrading to 8.44 and gzipping, regenerating and rebuilding, a non NT script no longer functioned. The firebug console was reporting that the code defining the occurrence of the script was not a function. Everything looked fine, but script was not included in the ALL.js despite being marked for that in WebServer object settings. Turning that setting off fixed the problem and later I included the script in ALL.js again without any problem.