Problems with Bowtie2 output

I have been using Bowtie2 on a collection of paired reads. While the Bam file looks fine, what I wanted was the file containing the mapped reads. This was empty, even though the log suggest it should not be. When I ran another job again the Bam file was fine, but the output file for unmapped reads gave me an error
" An error occurred setting the metadata for this dataset [Set it manually or retry auto-detection]". I found old post regarding the error message that suggested I could copy the dataset and use autodetect on the attributes, but in my hands this makes things really complicated the attributes keep changing!
I am not sure if this is specific to Bowtie2, but if there is not any easy fix maybe there is a better mapping program I could use. The attraction of Bowtie2 is the ease with which I can write the mapped and unmapped reads to file. Are there other mapping programs that will do this as efficiently?