Looks ok for me, but ...
#1- Is there a special reason to use subfolders of INBOX?
No, there is not.
#2- Are you sure, your IMAP server use "." as subfolder delimiter? Some servers use "/".
I don't know, but I can check it for you if you confirm me where to give a glance. I use VPS with Direct Admin configuration...
#3- It might be that you have screwed up accounts by prior configurations:
..... I mentioned that this stuff if case sensitive.
..... So if you had INBOX.spam in a prior configuration and now you have INBOX.Spam,
..... then INBOX.Spam won't be created and it fails to associate the spam folder icon,
..... because it looks for INBOX.Spam
Prior account and users usually did not create special folders o private configurations of the webmail. They are used to use Roundcube as it is
#4- Did you check the user preferences for special folder settings?
There are not, but in case, how to wipe all and set a brand new configuration for all the hundreds mail accounts? I would really prefer start up once again...
Regarding the screen shot of your Folder Settings I guess that your server use "/" as folder delimiter, otherwise you should not see f.e. INBOX.Drafts in the folder list.
I don't know...