This may happen if you are using a role in 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.