The API you're referring to is only for creating and updating custom object records, we do not currently offer an API for managing custom object types.
Sorry if I was unclear, but I'd like to see some of the example requests and responses where you're observing this behavior, rather than just a description.
Possibly a silly question, but when making a request for a new page, are you passing the value of "nextPageToken" from the previous response into the new request?