SAP Search does not result all navigation points

Hello,

Portal version: CE7.3

We have customized masthead and are using SAP Search functionality to get suggestions for navigation points.

We are using a custom AFP which is created as a delta link from standard AFP.

We posted this issue to SAP and they suggested to check if issue occurs with SAP standard AFP. We noticed that it does.

Any ideas/suggestions that might help?

Does it have to do anything with custom theme we are using? (i dont believe it so, but still,  just wanted to confirm).

Thanks & Regards,

Amey Mogare