As title says, one of the latest updates to clist_modern changed the behavior; it now doesn't put offline contacts on the bottom of the list, and the checkbox "don't put offline contacts on the bottom" makes no difference. I assume it is a consequence of the many changes to clist_modern as of late.
EDIT:
I noticed it works fine if I use "Status" as one of the "sort by" options. But it should not need to be the case since offline contacts should always be at the bottom.