Further investigation into the log files showed that "Proper pairs" from RSeQC bamstat are 43.73797, Total records are 86.153242, "Unique" are 43.741755. The definition of "Unique" is "mapq >= mapq_cut (unique)", i.e. all the read numbers are after filtering of the reads with mapq_cut, which is by default 30. So the statistics are actually only for reads with MAPQ >=30.