bowtie2 version 2.1.0 pairedEnd mappings with params:
--end-to-end --no-mixed --no-dovetail --no-contain --no-overlap --no-unal
I specify --un-conc to get unmapped reads, but the resulting fastq files are nearly empty.
Using version 2.0.5 all the expected unmapped reads are present. I have not tried intermediate versions.
I will send Ben examples by private email.