My Wordpress website broke with 404s all over the place, so I reinstalled Wordpress, again, yesterday morning. I decided to install only the plugins that I deemed absolutely necessary and let the more complex ones (e.g. WP Super Cache) at their default settings, without customization.
My website it's been working fine for a while now (it was taking less than 4 hours to brake as I customized it before), so my guess is that certain custom settings from WP Super Cache (maybe the use of mod_rewrite instead of PHP to serve cached files) or Better WP Security (I didn't install it this time) might be causing the Polylang plugin or the whole Wordpress installation to brake.
It's working fine using the language code (/en/ or /es/) added to all urls when using pretty permalinks, as it is your recommended setting when using Yoast SEO. The permalink part for the WP e-Commerce pages titles switch to English, when containing a post, but that's something that I can live with.
I've set up a localhost mirror copy of my website in my mac, using it's native Apache and PHP installations, and I've been going through it with Netbeans, but it takes a lot of time to debug a system so big and complex, and sometimes time is limited.
That's why, Chouby, I totally understand and respect the work you've been doing with the Polylang plugin. We just hope that you get the time to fix these situations at a later release.
Thank you, Chouby!