Thank you for the additional details related to the issue that you are faced with.
May I please ask you to let me know if you have used OAuth authentication during your project creation?
If yes, in this case, the IDE connects to your org every time when you open the project. And this can be a reason for the error.
If you have used regular Salesforce credentials (login, password, and security token if this is necessary), I kindly ask you to reproduce the issue one more time and send us a bug report with attached log files directly from the IDE - you can find this functionality in the menu help -> Report a bug, please specify your email and enable the 'Attach Log File' checkbox.
This way we would receive your TWS logs which can help to get an information about the error.