If that is your entire ModuleManager.log, then MM did not do anything at all, between "Pre patch init" and "Done!" we should be seeing all the patches applied by it.
Or just a guess, do you happen to have ModuleManager by Lisias? In that case there should be a kspe.cfg file somewhere in GameData or a PluginData folder under the game's root folder, and you should set LogLevel for ModuleManager to 3 or higher (5 is the highest). I genuinely don't get why it would be suppressed by default, but either somehow the log messages are hidden or ModuleManager does not do anything at all. This is seriously not a normal ModuleManager.log for a modded game...
