Wow thanks. This explains a lot
Today I've been testing a composite sync input upgrade for the GreenAntz transcoder (so you can feed it csync via VGA as well as H+V).
Just found out that if you tick that "Add modes from mode list" box and are swapping between composite sync and H+V sync, frequently changing polarities and regenerating modeline installs, you can end up by default in this "640x480@30i" mode. Which I think is what Calamity is talking about. The modeline looks almost the same as "640x480@60i", including polarities, except under the oscilloscope where you can see the vertical part of the CRTEMU generated composite sync is inverted (positive). It goes the wrong way for normal csync. It can leave you with an unusable desktop on a TV, making it difficult to sync and fix things.
Don't know if that is a bug, but now I know don't tick that box!