My point is that I am a researcher (in quantum information theory) and I've published a couple of papers on quantum computing which talk about algorithmic complexity. In once case I've been told to by an editor to change run time to runtime, and in another case I've been told (by an editor at a different journal) to change run-time to run time.

There isn't a fixed consistent usage, even in the academic literature. More importantly though it doesn't matter which you use, as long as its obvious what you're talking about.