Hi @Vixer, let's assume your demux process via Mr. DNA's software is okay.
Here are the quality score boxplots for your data:
Here are the quality score boxplots for "typical" Illumina Paired-end data:
The narrow band of high-quality scores in your reads seems pretty suspicious to me --- it looks like some kind of quality filtering has already been applied to these data, since they don't exhibit the "typical" error profile one would expect to see. Anyway, keep us posted! 