I am trying to convert a classic application to lightning, in the process i got stuck with a wired issue.For a particular user one child object's related list item is not getting displayed in the related list section. But the same related list item is getting displayed when user switched back to Classic Mode.
I checked all permissions for the particular user profile like:
Am I missing something here, or is this a bug in the instance?
I had a similar issue with the Partner and Activities related lists on the Account page layout from classic to lightning. I found that the Partner Account related list is not available in lightning and the Activity related list was split off into a new component. This could be the same issue you are having however I can't be sure without knowing what object you are missing from your lightning page layout.
As you have mentioned that it is custom object, please check this KB article :https://help.salesforce.com/articleView?id=000249344&type=1