I am able to reproduce the issue.
I removed all security roles from my account except for one to test with.
With Org Level Access Read to Opportunity
Flow fires correctly on Update of an Opportunity
Any other permission level (User Level) for Read to Opportunity
Flow fails with the 'Crm instance does not have security roles defined for you.' I have permission to the record i updated via the CRM UI but Flow fails with the security error above.
It appears though without Org Level read access to the record type you want Flow to trigger on, Flow will fail.
