The penguin logo is not the default N900/maemo boot screen, and there is no official way to change it within Nokia-supplied settings. You must have customizations that were reset to default. You'll simply need to remake the customization.

As to the other two apps, I can only suggest you uninstall them and reinstall them to see if there's any change. If that doesn't help, take a look in their respective forum threads to see if anyone else had those problems.