Hi Aamir,
Few things here. First the LDAP options in SDM are NOT for authentication, they are ONLY for importing/updating users, so that is not related to the authentication timeout you are having. Your issue looks more like a performance issue of some sort - which could be on the SDM side OR the EEM side. I am guessing your EEM is connected to an LDAP or AD server to authenticate the users. If so, then most likely the delay is on the EEM side where its taking EEM a longer time than usual to get that user authenticated, and thus it takes longer to get the authentication token back to SDM resulting in that message. Now I cant say for sure, but this is just a hunch based on what we know. What I would do is right when the problem occurs, attempt to log into the EEM UI directly as the same user and see if there is any delay. You can also look at the EEM logs to see if there are any timeouts or "unable to connect..." type of messages.
If that does not yield anything, then I would say to open a support case and an engineer will troubleshoot the issue with you.
Hope this helps a bit.
Thanks,
Jon I.