After adding a new organization, you find that sometimes, when creating an invoice for an item, it attaches to another organization instead of the one intended.
This could be due to a delay in the system in the user creation and association with the Organization you created which is why you were not having the option to choose that org in the previous attempts.
To solve this issue you must void the existing item and generate a new one. This can be done by using the article: OnDemand: Creating, Editing, and Voiding an Invoice.
If you need further assistance, please create a support ticket and include a screenshot of the invoice with the name of the organizations concerned.