Thank you for contacting Sitefinity support.
The version of the configs will stay unchanged if the module related to the config is deactivated. Otherwise they should all increase the version.
Can you please tell me what configs are with unchanged version numbers so we would be able to conclude whether they may affect the application.
The version of the configs is the actual version of the module. It does not dictates an upgrade behavior. The versions of the modules in the SystemConfig is the driving force for upgrade, i.e. if the version of the assemblies is higher than the version of the modules in the system configs thank an upgrade will be initialized (for the particular module/s). This upgrade will also upgrade the schema version of the database (it cannot be downgraded! - always do backup of the database before upgrade).
If the upgrade of some module has failed - an error message will be present in the SystemConfig. The upgrade can be restarted by removing the error message (or lowering or removing the version number) and recycling the application.
Not upgraded version of a config (if no errors on the website are noticed) means the module was not accessible (disabled, uninstalled, etc.).
We still haven't publicly described the "behind the scenes" process of the upgrade, but soon we should publish such a resource, because it seems it will be valuable for the clients.
About your issue, you still did not tell me what config files' versions did not get upgraded. We will need that info so we can tell you whether it's serious or not.
1. Go to App_Data -> Sitefinity -> Configurations -> SystemConfig.config
2. Remove the Synchronization module version. For instance:
<add name="Synchronization" />