Amazon S3 CDN uploads to wrong path

Hi,

i switched from Multisite with subdomains configuration to Multisite with subdirectories configuration.

One thing that stopped working is Amazon S3 CDN via W3TC plugin.

Basicly what happens is that W3TC upload files to this path:
cdn.mainsite.com/subsite/wp-content/uploads/sites/ID/2016/10/some-picture.jpg

while the content on the website is actually displayed from here:
cdn.mainsite.com/wp-content/uploads/sites/ID/2016/10/some-picture.jpg

W3TC creates a /subsite directory on amazon s3 which only visually exists (because of permalinks) but does not exist on my server.

Any ideas?