This may happen if you are using a role in the Gmail app and that does not have access to Custom Records. It can be resolved by adding the Custom Record Types permission to the role and that should enable access to Custom Records in Global search as well as record filters. 

To enable access to custom records, go to Setup > Users/Roles > Manage Roles

Select the Role you wish to modify and click Edit.

On the Permissions sub tab, click on Setup. In the permission, list add Custom Record Types  with Level View and Save

Did this answer your question?