And this is exactly why I'm trying to find a new place to work. I finally realized after a few years that I need some real mentorship to be fully competent in a research environment (even after an MS), and four years of "trial by fire" in a lab which generates data from a ton of tiny experiments (rather than a few larger experiments) with 100 biologists and only two of us bioinformaticians, and a pile of ten years worth of old microarray data that no one has any sample annotation for (but it's invaluable!)-- was less of a constructive learning experience than it seemed like it was going to be. I need to find/create an environment that will allow me to use the motivation I know I used to have for this.
So for anyone from a CS-oriented background, or who is thinking of doing a degree program in bioinformatics that isn't oriented around research- try to help out in various labs, and find a good mentor. See what environments work best for you, and what sort of problems you want to apply yourself to. The field is developing far faster than most college programs can move, but by getting out there and seeing what skills/knowledge will actually be useful, you can work on filling in the gaps sooner.