Please include a version number of BLS-2016 (28.0x.##) in the event that a recent software update may be involved in an issue.
With your rules, at the left are several tabs, one of them reading "Vacant Players". Click on that and look at the section named "Individual Match Points for Vacants".
For the first item, you probably have that set to "No points are awarded...." You probably should use the option "If absent/vacant player wins, points go only to team winning the game."
You will also want to look under the "Absent Players" tab, which will have similar questions and answers under the section "Individual Match Points for Absentee".
Always check, download, and install the most recent update of your software to ensure that issues may have been corrected.