Bowtie preference for earlier alignments?

[WHP]

So, I aligned my small RNA reads using the following command in bowtie.

bowtie -S -a -v 1 -m 1 --best --strata Reference/Release4.3/dmel_rel4_3 2012/fastq2012/Adap_len_rRNA/A_final.fastq --max A_BDGP4_3_multireads.fastq A_BDGP4_3.sam

The reference is for Drosophila chromosomes arm sequences. If I grep for the title I get this.

>2L type=chromosome_arm; loc=2L:1..22407834; ID=2L; release=r4.3; species=Dmel;
>4 type=chromosome_arm; loc=4:1..1281640; ID=4; release=r4.3; species=Dmel;
>2R type=chromosome_arm; loc=2R:1..20766785; ID=2R; release=r4.3; species=Dmel;
>3R type=chromosome_arm; loc=3R:1..27905053; ID=3R; release=r4.3; species=Dmel;
>X type=chromosome_arm; loc=X:1..22224390; ID=X; release=r4.3; species=Dmel;
>3L type=chromosome_arm; loc=3L:1..23771897; ID=3L; release=r4.3; species=Dmel;
>dmel_mitochondrion_genome type=chromosome; loc=dmel_mitochondrion_genome:1..195


I then used multiBamCov to find read counts for my regions of interest (~500) which are evenly distributed throughout the chromosomes. But, I find that ALL the alignments which match my region of interest are in 2L and 4. I know it could be that the coordinates are off for all the chromosomes except 2L and 4, but then I wonder whether there could be anything forcing a preference for alignments that happen earlier in the reference file (since 2L and 4 are the first chromosomes)? Any other problems I should check for?