I had the same situation. I worked for in a hybrid software engineering/operations role for a large Internet firm, while studying part-time. It was a great and challenging position, not just due to its content (how do you deal with running tens of thousands of nodes in clusters distributed throughout the world?) but the people and the environment (it was one of the few places where you could find people in an operations team hacking OCaml).
Ultimately, I was found by a start-up and left, seeing greater responsibility and compensation. Six month in, I started looking around. The lack of mental stimulation scared and de-motivated me. I switched jobs to a non-web-centric software engineering role. It felt "scary" ("job hopping" as the country headed into the recession?), but it was the right choice.
The risk is thus: if you're bright, it's very easy to become good at most anything. Some fields (systems administration, web development) can be fun (given the right environment, e.g. the operations team I've described) and are always in high demand. None the less, if you become good at something you don't ultimately find challenging and worth-while it can be a risk further down on.
Have you consider going into scientific software development? Both your web development background (the web is the user interface these days) and your scientific education will be of help. You might take a paycut, you may not have the flexible hours, but the job might provide both the content and the environment (i.e. the people) that will keep you sharp.