So I have some additional information. As a new user attempting to set this up as an alternative to dotproject it would be good to get some feedback.
Bottom line: I have gained access to my OpenGoo installation despite the 406 errors by manipulating the cookies.
When I clear the cookies set by my domain and visit the OpenGoo login before visiting any other location on my domain I have complete access. It is fully functional. I can then log out and visit any other area of my domain without a problem. I cannot go back to OpenGoo though. A 406 error occurs and the domain is blocked until I clear cookies again.
To access OpenGoo: clear all cookies. Go directly to OpenGoo log in. Full access to OpenGoo. Leave OpenGoo, full access to domain, but cannot return to OpenGoo without clearing cookies.
Just to be clear, OpenGoo is not accessible if I attempt to access after visiting any location on my domain first without clearing the cookies set.
Is this of any use to diagnosing what is going on?