When upgrating from 4.4.6 to 4.5 we have the possibility to run the migration script within the upgrade process, or to perform a normal module upgrade (from 4.4.6 to 4.5) and later call the migration script from the Groovy console.
This issue only happens in the second case.

The first step of the migration process is to move and rename nodes (for example: Component templates (former paragraphs) to config:<module name>/templates/components).
In this case, we will face (tons of) WARNings like:

2012-03-12 12:43:42,593 WARN gnolia.content2bean.impl.Content2BeanProcessorImpl: can't resolve class for node /modules/standard-templating-kit/templates/stkArticle
java.lang.ClassNotFoundException: info.magnolia.module.templatingkit.templates.STKTemplate
....

In fact info.magnolia.module.templatingkit.templates.STKTemplate does not exist any more.

IMPORTANT.
Once the migration script ended and Magnolia's restarted, the migrated Magnolia is running fine.