What I realized when upgrading Project Open from 5.1.5 to 5.3 is that some of the content repository upgrade scripts are failing, because the installed kernel version is newer then the one expected during the upgrade. So don't worry if some of them fail, it will all be dealt with just fine by the last upgrade script.
Not sure though what to do in general in a situation like this... When an upgrade script (e.g. 5.2.0d16-d17.sql) assumes a acs-kernel to be in a certain state, which it is not after it has been upgraded e.g. to 5.3.0.
