1. 40 is not an adequate sample size. Not even close.
2. Continuous text entry in LaTeX and Word is very similar, so why are LaTeX users far behind Word users here? Did the researchers measure typing speed and control for that, so that the Word group wasn't given a set of typists who were, on average, faster?
3. For the equation entry portion, did they control for user expertise when assigning participants to groups? e.g. Asking a psychologist to typeset a physics equation is going to result in slower work and more mistakes. With a sample size of 40, an imbalance of just a person or two could easily throw the whole study off. (Note: They did find that LaTeX was better for equations, which is not surprising. Their methods are still suspect though.)
4. This study does not address the specific tasks most people use LaTeX for: papers and books. Both are longer than a quick and dirty copy job, and such jobs benefit greatly from LaTeX's ability to produce consistent output when edited. Word documents break in all sorts of strange ways once they become long and complex enough.