Thank you for sharing this with us.
I kindly ask you to check if all of your custom objects are available in the Schema Explorer panel (you can open it from the menu View). Here we show all the objects that are available on your organization even if they are absent in your TWS project.
Also, can you please check if you have the enable 'Subscribe' command in the Project Metadata Components wizard. If it is not active, please enable it and pull from Salesforce one more time.
If this won't help, we would appreciate if you could send us bug report directly from the IDE - you can find this functionality in the menu Help -> Report a Bug, please put your email and enable the 'Attach Log File' checkbox. This way we will receive you TWS log files that could help us to find a reason why not all objects are available for you in your TWS project.
Looking forward to your response.