There are gaps in Custom report of NFA when there is a conversation filter.
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The problem could be of either there is no conversation data during the time period for which you see the gap or the conversation is not in TOP N list.
To confirm the problem, you can run flow forensics report for the time period during which you see the gap in custom reporting and check if there is any data.
This is working as designed for as there may not always be data being transmitted between two hosts at any given time, or that data may not be part of the Top N Hosts or Conversations data.
Contact CA Support if you have further questions regarding this.