Did you take your own en_us.php.php (or another language file)?
the problem is in the lang file, it that does not have the required labels for the menus (or not all of them).
See here: https://github.com/rathena/FluxCP/commit/8f95e74259864edb7ed188ee38f7f4c3815a8ca9and here https://github.com/rathena/FluxCP/commit/1f8165dfc5d3109136294cf5815a300a5bd9711c
There is a "new" method to set the labels that allows to translate them, but gives that bug when the labels do not exist.
Anubis-K's post in Flux Menu Empty was marked as the answer