Extensiv Integration Manager is raising the following alert when trying to mark your orders as shipped:
This issue will also cause Integration Manager to miss orders because WooCommerce does not return an error message when we download orders. After resolving this issue, you must contact Integration Manager support to have any missed orders re-pulled.
This issue is usually caused because your WooCommerce API user is not an administrator. To fix this:
This issue can also be caused by your WooCommerce server settings blocking or removing certain header data required by the WooCommerce API.
To solve this issue, you must correct the Basic Auth header. In Apache this can be done using a rewrite rule in either your Apache config file, or in the WooCommerce .htaccess file:
RewriteEngine On RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
WooCommerce may overwrite changes you make to your .htaccess file. Contact WooCommerce support if you continue to have trouble with this issue.
This article explains the issue and several possible solutions: https://github.com/WP-API/Basic-Auth/issues/35