This might be an issue between plugins. The filtering capability is not part of Roundcube and is provided by the filters
plugin. I think the filter rules end up running after the message has appeared in the inbox briefly and then it gets moved after the notification has happened.
By default we have "check_all_folders" turned off which you can confirm by going to Settings >> Mailbox View and confirming that "Check all folders for new messages" is unchecked.
Is the check all folders option disabled on your account?