By updating to version 1.24 the  BuildOn column plugin will be installed as a dependency. This plugin causes severe performance problems on instances as big as ours and brings Jenkins down to a total freeze over night. Downgrading to 1.23 and removing the  BuildOn column plugin fixes the problem.

BTW, the mentioned plugin is very old and maybe orphaned and was replaced by the extra columns plugin. But maybe the displaying of such extra column information should be optional because these columns can be real performance monsters on large installations.