Since we ran "transition" in CRM 2013 online, user names are changed.
I tried to re-configure the CRM adapter in Connector for DynamicsV3.1. At the get organizations step, I got the "Did not find any organizations." message.
The CRM discovery service is still "dev.crm.dynamics.com/.../Discovery.svc", right?
The CRM admin account and password is correct, I can sign in CRM.
I tried using the CRM admin account and CRM integrator account to test the CRM setting, both failed.
In CRM 2013 the discovery service in now: disco.crm.dynamics.com/.../Discovery.svc not dev.crm.dynamics.com. You can find this by navigating to: settings\customizations\developer resources. You will still want to use a non-administrator account for the CRM adapter user and you should not have to re-configure anything after the upgrade.
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Connector for Microsoft Dynamics team blog
Try to login using integration account, it might tell about login problems.
Share the screenshots if possible.
Please mark my answer as correct if you find so.
You cannot login to Dynamics CRM online with the integration account as it is non-interactive. In Dynamics CRM on-premises you can log in using that account but it is not recommended since any changes that you make to data in Dynamics CRM will not be picked up by the integration.
For Dynamics CRM online you do not need to provide a port nor a domain, just the user name for the integration user, not the administrator for the organization in the adapter settings windows.