Sorry, my fault.
The plugin works fine even if a custom uploads directory is used.
My problem had to do with the number of files already present in the custom uploads folder that caused a timeout error.
Just updated to the latest version, but the weird problem persist.
Opa! Just got it!
It’s just that some time ago I had the idea to set a rel canonical on this category pointing to the its unique post (seemed like a possible duplicate issue to me: a category page with its posts abstracts having much similar content with its unique post).
I removed the canonical and now the sitemap is OK.
I wonder, however, was this a correct behavour of your plugin?