RNA-seQC negative mean per base coverage and figures are not generated correctly

Question

[jeremy]

I am using RNA-seQC 1.1.7

1. RNA-seQC gives negative "Mean Per Base Cov." for some of my samples, which doesn't make sense. Is this a bug?
2. Because the my sample name is long, the mean coverage figure for high, medium, and low expressed genes only show the legend. Is there a way to make the figure correctly?