Looks like HaplotypeCaller is missing variants that are <16 bp from the end of the read (possibly even more, have not studied systematically but found a GATK forum thread discussing this same issue).
Therefore, reimplemented calling by UnifiedGenotyper
Reference: http://gatkforums.broadinstitute.org/discussion/3499/haplotypecaller-doesn-t-call-true-variants-which-are-located-on-the-outside-of-duplicated-reads
fixed bug