I edited my subtheme .info file to add a reference to a custom Javascript file, following the instructions here: http://www.webbykat.com/2012/02/adding-custom-javascript-omega-subtheme-....

After I enabled it using Toggle Libraries and clearing the cache, I checked my homepage and a number of zones - the prefaces and postscript zones specifically - disappeared. They aren't being loaded at all. The branding, menu and header zones get rendered, then it skips straight to the footer zone.

This only happens on the homepage. On every other page the postscript zones uniformly display, as do the content and sidebar zones.

Deleting the references to the Javascript file in the subtheme .info file doesn't fix this.