Tophat 2 - Both Pairs Map Concordantly

Hi,

I have just run the following command

tophat2 --solexa1.3-quals -p 12 -r 80 --max-multihits 1 --no-mixed --no-discordant /home/Turkey/Index/turkeyindex /home/Turkey/WTCHG24920061sequence1.fa /home/Turkey/WTCHG24920062sequence_2.fa

I understand this is instructing Tophat 2 to map the reads so that no multiple hits are allowed, and both pairs of reads have to map concordantly.

However, when I examine the stats of the output in Bamtools I get the following

Total reads: 33102389
Mapped reads: 33102389 (100%)
Forward strand: 16600010 (50.1475%)
Reverse strand: 16502379 (49.8525%)
Failed QC: 0 (0%)
Duplicates: 0 (0%)
Paired-end reads: 33102389 (100%)
'Proper-pairs': 28865628 (87.201%)
Both pairs mapped: 30696760 (92.7328%)
Read 1: 16559354
Read 2: 16543035
Singletons: 2405629 (7.26724%)

Why do only 92.7% of the reads fall under both pairs are mapped and 7.2% are singletons? I would expect there to be no singleton reads and 100% where both pairs have mapped, given the options I specified?

Any help would be much appreciated.

Thanks