Offline Contribution receipts does not contain custom fields information
I don't think the receipt template for off-line contributions includes the tokens/code to pull in the custom fields. You might want to compare your templates for each - https://www.domain.com/civicrm/admin/messageTemplates?reset=1 and select System Workflow Messages - and compare the two. Then you can attempt copying/pasting in code from the online template and test the email that goes out.