Hi Matthew,
Are you using CLJS? The most likely culprit is that you have your CLJS output directory as part of your project, so when you switch to FF your files are saved and compiled, and when you switch back to IntelliJ it notices a whole bunch of new JavaScript and indexes it. Cursive tries its best to automatically exclude these directories for lein projects, but that’s much harder with the new quickstart-style projects. Find the directory that your JS goes into and in the project view, right click->Mark Directory As->Excluded.
If that’s not your case or that doesn’t help, let me know.