The solution to the problem that works when I have this problem with customers.
1. Generate a new token for Omnissa Workspace ONE Access. (if you have this symptom, you need to re-generate the token, you can't use the token again)
2. You need to prepare the public keys of the Root, Intermediate certificates signing the FQDN address of Workspace ONE Access.
3. You choose the advanced installation of the Agent and upload the certs and the new key. It solves the problem in 99% of cases.