I believe the issue is the shorter stay usually processed before the longer stays end.
For example 1st and longer stay : 1-20Nov
and 2nd and shorter stay are : 7-9 Nov

on 9Nov the system process the point n nights
then on 20Nov they recognise that there is an overlap reservation and reject the longer stay.

And for multiple room points, I usually booked them in 1 reservation or combine them when check in and put the entire charge on my personal room folio.
No issue so far with points earning.