Have you referred the following reference for custom top registration
Creating a Custom Application in Oracle E-Business Suite Release 12.2 (Doc ID 1577707.1)
Create And Register CUSTOM Schema On EBS 12.2 (Doc ID 1929668.1)
Does the required entries exists in both the nodes as part of custom top registration
We are on ebs R12.1.3, does the Doc ID's applicable to this version as well?
You may refer Customization Standards in Oracle E-Business Suite Developer's Guide for EBS 12.1.3 version