I have narrowed down what appears to be the cause in the USP_SIMPLEDATALIST_BBNCSPECIALPAGE stored procedure. It appears to be with this line:
insert into @PAGES exec dbo.spGetSpecialPages 1, @INCLUDELOCKEDARTIFACTS
The 1 is calling the primary site.
When running exec dbo.spGetSpecialPages 1 in sql the results from the primary site appear.
If you then change it to exec dbo.spGetSpecialPages 2 the results from the second site will appear.
Download and install the latest patch, which contains all fixes from previous patches. If you are running an older version, download and install the latest version and then the patch.