The reason I explained above is not the cause of the issue. Even in my local fluentd, the logs shows that an extra "\" will get applied. So not the cause of it.
After further ;looking into the config maps of the Kubernet connect I have noticed that all the /var/log/containers/*.log configs are hard coded and does not support the multiline. The multiline option is only for other logs which are not part of the /var/log/containers/ folder.
If anyone else have any ideas of doing it please let me know.