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I see that both you and the other user had non-standard installation environments, so it makes it difficult for us to determine - and I wonder if this might be part of the issue. So far we at Artefactual have not encountered this issue with Ubuntu and Nginx.
One question - are you creating a brand new database in the new 2.3.1 installation, before loading your sql-dump? This is an important first step - essentially, you have to follow the installation instructions as if you are installing a brand new AtoM instance for the first time. My only theories at present are that either some dependency is missing on your particular installation environment, and/or some step of the upgrade process was not fully completed.
mysql -u username -p -e 'drop database new_database; create database new_database character set utf8 collate utf8_unicode_ci;'
rsync -av /var/www/icaatom_old/uploads /usr/share/nginx/atom/uploads
rsync -av /var/www/icaatom_old/uploads /usr/share/nginx/atom ?
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