Menu link Translation I'm using i18n and submodules to translate an English Language site to Spanish. I'm also using Automatic path aliases.

The issue is that menu links are directly to the node: node/42. When in the Spanish part of the site, /es/ the links take me to es/node/42, not to the aliased url.

The best answer I've seen is this "Afterwards, you can arrange your menu links as you need them. I use parent/child URL aliases based on menu hierarchy, so I make a mirror menu tree." I don't know what he means, but it sounds like what I'm trying to do.
Your problem might be because of the "language detection" configuration. 

So check this configuration via Configuration -> Languages -> detection and selection: the order should be 'URL, Default, User', and not something like 'Default, URL, User'.