I'm not sure if this is a Bee issue or something else, but the issue only happens when running Bee.
Running Bd 1.28.2, Bee 1.x-1.0.2.
The site runs fine without problems afaik.
bee st works fine.
bee cron and bee pml throw this error:
Exception: The configuration directory in settings.php is specified as './files/config_9c5e4e5663bfc5ea8eca0ce92b9bca01/active', but this directory is either empty or missing crucial files. Check that the $config_directories variable is correct in settings.php. in _backdrop_bootstrap_configuration() (line 3064 of /srv/www/profess/backdrop/core/includes/bootstrap.inc).
There's nothing in the recent log messages.
Calling cron with curl or in a browser also has no issues.