Hi Martin,
After discussing this issue with our developers, we feel that it's best to do a clean install/upgrade of LabKey.
Essentially, you would be doing the following:
1. Unpacking the tar.gz install file you downloaded before
2. Finding your existing labkey installation
3. Stopping Tomcat, then MOVING the LABKEY_HOME/labkeywebapp and LABKEY_HOME/modules directories to a backup folder
4. COPYING the tomcat_home/lib and tomcat_home/conf directories to the backup folder
5. Creating new LABKEY_HOME/labkeywebapp and LABKEY_HOME/modules directories that are empty (this ensures that no old modules interfere with the upgrade).
6. Accessing that unpacked tar.gz and copying the contents from its labkeywebapp and modules directories into the same named directories you made in Step 5.
7. Copy the contents of the tomcat-lib directory from the unpacked tar.gz and put that into the tomcat_home/lib directory and overwrite any existing files.
8. Restart Tomcat and check LabKey to see if the changes went through and whether the error still appears.
Note: Although technically we recommend making a fresh new labkey.xml file within the tomcat directory under tomcat-home/conf/Catalina/localhost/, I think that won't be necessary here.
Full instruction is in the article below:
https://www.labkey.org/home/Documentation/wiki-page.view?name=manupgrade
I think if you go through this clean upgrade, this should remove that error you were seeing.
Give this a try and let us know if you run into any issues or have any further questions.
Regards,
Jon