Two installs, permalinks structure not working

Hello,

I’m having the same issue here:
http://wordpress.org/support/topic/139383

I’ve got one install on the root, and another one in a folder. Each install has its own database.

It works with the default Permalink structure. But as soon as I try to customize the permalink structure, any permalink points on my root install (404 error, of course).

Any hint on how to get those permalinks customized without breaking the whole thing, please?

Thanks in advance.