Another thought (as I edit a document that a co-author wrote): if you could mimic tcilatex.tex (which Scientific Workplace throws into any document it touches) in a minimal, nonintrusive way, that would be fantastic. (tcilatex seems to be changing the 'gather' environment so that individual equations can no longer be numbered, for example.)
OK, we'll have a look. For now, you can upload tcilatex.tex to writeLaTeX and then \input{tcilatex.tex} after your \documentclass line. (Note: it seems to conflict with the amsmath package, however.)