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Why is CF11 RTM + CU5 drastically different from the latest deployment package + CU5?

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We have a development copy of CF11 that we installed as a RTM build that has since gone through CU1 through CU5.  We just recently installed CF11 on our production server which was done from the latest deployment package and was then upgraded to CU4 then CU5.  We've noticed instabilities with the production copy that we haven't seen once on the development copy the years it has been running.

 

The most common are "Error Executing Database Query. Timed out trying to establish connection" errors at random while other applications using the same DB server have no issues at all.  If you reload the page the DB call goes through the 2nd time.  Only CF applications on this web server have these issues and not .NET or Java based ones.

 

So wondering if I had configuration wrong I merge compared our development versus production server and found a number of core parts of the CF11 that started as RTM to be much older.  Various jar files, the Jetty runtime is v6 instead of v9, tomcat files, etc.  It's obvious at some point the CF11 deployment package has been updated but typically in the past we'd see a CF 9.0.1 type of release for major deployment changes but both of my servers report as being Version 11,0,05,293506.


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