I noticed the same problem when running pileup under SAMtools-0.1.15. However the problem does not seem to occur when running pileup under SAMtools-0.1.4 (using the same reference file, same BAM file and same command line options).
samtools-0.1.4/samtools pileup -s -f reference.fa sorted.bam > pileup.out
samtools-0.1.4/samtools pileup -s -f reference.fa sorted.bam > pileup.out
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