unexpected bowtie2 unpaired alignment behavior

Hello

I am using Bowtie2 2.2.3.
It is my understanding that when Bowtie2 cannot align paired end reads as pairs it will attempt to align them singly. If this is so can you explain the following results which I have repeated several times with and without the --non-determinant flag (as suggested on Biostar). Note that this test dataset contains only 552 PE reads for which I expect one unpaired alignment.

Thanks

Mark

[rosema1@demeter bowtie2]$ bowtie2 -x 12274_pmi.fa --local -N 0 -L 25 -p 1 -1 s_2_1_25_PMI.fq -2 s_2_2_25_PMI.fq -S s_2_1and2_25_PMI.fq-vs-12274_pmi.fa.sam -I 0 -X 750 --score-min G,5,0 -i S,1,0
278 reads; of these:
278 (100.00%) were paired; of these:
278 (100.00%) aligned concordantly 0 times
0 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
278 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
278 pairs aligned 0 times concordantly or discordantly; of these:
556 mates make up the pairs; of these:
556 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate

[rosema1@demeter bowtie2]$ bowtie2 -x 12274_pmi.fa --local -N 0 -L 25 -p 1 -U s_2_1_25_PMI.fq,s_2_2_25_PMI.fq -S s_2_1_25_PMI.fq-and-s_2_2_25_PMI.fq-vs-12274_pmi.fa.sam -I 0 -X 750 --score-min G,5,0 -i S,1,0
556 reads; of these:
556 (100.00%) were unpaired; of these:
555 (99.82%) aligned 0 times
0 (0.00%) aligned exactly 1 time
1 (0.18%) aligned >1 times
0.18% overall alignment rate