With your background you are unlikely to get a research job in bioinformatics. Think of it this way. A MSc program is at least 1 year long. The course you took is 5 weeks.
You are more likely to find a support position, writing software for a bioinformatics group.
Pay is typically lower. As you point out, most people hiring are at universities. Further (and my experience is out of date so it might have changed), in general programmers are typically better paid than researchers. In science-oriented companies, the decision makers are often people with a science background, often PhD, so often 6+ years of graduate school.
It can be hard for them to accept that someone with a BS + 2 years of work experience has a market value higher than a newly minted PhD.
I haven't done bioinformatics for a long time, and I never did much in the first place. My experience was that the typical problem solving is "parse the output of program X so the output can be fed into program Y". This was back in the days when Perl was the main programming language in bioinformatics.
