It’s a bug in MODX that was introduced with version 3.1.0.
I created a issue for it on Github:
Basically the files used to be sorted by the timestamp (which is a number).
Now the files get sorted by the already formatted datetime-string. This only works correctly if the default system setting values are used (like Y-m-d for manager_date_format). But fails when other values are used, as the sorting is now alphabetically.