Hi Kyle,
I suspect that the BAM file from which the reads were extracted was sorted by coordinate.
This causes the problem for STAR sorting, since STAR uses the first 100,000 reads to define the sorting bins, expecting the reads to come from random positions on the genome.
Ideally, to solve this problem, you would need to randomize read order before mapping - I think you can use samtools bamshuf command will do it for the BAM file before Picard converts it to fastqs.
Alternatively, if you have enough RAM, you can try to increase the sorting memory, for this particular sample --limitBAMsortRAM 33000000000 .
In principle, you can set it to your EAM amount minus a few GB.
Cheers
Alex