I'm calling variants using three input/reference files (dedup.bam; genome.fa; and chr17.cds.bed) and creating two vcf files, (1) for gatk.vcf and (2) freebayes.vcf.

GATK returned more variants (POS) and more dbSNPs.  Scanning the files you quickly notice the different quality scores between the two files, with far greater range in QUAL (super low and high scores) found in the freebies.vcf file.  What factors contribute to the higher variant count in GATK vcf files compared to freebayes?
Keep in mind that the GATK variant callers are designed to be as sensitive as possible and will therefore include many false positives, so you need to apply some filtering steps after calling to remove those false positives, as described in the GATK Best Practices. It's essentially impossible to answer your question without knowing more about how you did the variant calling in both cases, and what kind of filtering and evaluation you did on the results. 

It's also important to understand that QUAL scores are calculated differently by different variant callers, so it's tricky to compare them directly. You'll get more insights from evaluating your results relative to known callsets or truth sets. 