The problem has been resolved. Essentially, the problem was due to NETLOGON failures whenever the Security server needed to check with Active Directory whenever a domain resource was used such as checking the machine account when logging on. I suspect the ultimate cause to be some sort of corruption or problem in RPC processing on the Security server. I never did determine the actual cause of the problem but it turns out the problem started just after I installed the DPM client on the security server.
The easiest solution was to re-install the server. EBS has a feature where when you install one of the three servers, the wizards will check with active directory and determine whether the particular server you are re-installing was a member of the domain previously. This only works if you give the server the same name as it previously had and you must have at least one DC available. It asks you if you want to replace the old server configuration in active directory with the one you are installing and then proceeds to do so, successfully I might add. Given that it was the security server and there was very little changed from the default configuration and no user data involved, it was a painless quick re-install. It was intelligent enough to re-establish it's role including installing the certificates. All I had to do was add the 6 rules I had defined back into TMG and make a few other minor config changes for connectivity verifiers. I was confident of the server successfully re-joining the domain because I had tested this exact scenario when I first installed EBS by destroying active directory on the management server and then re-installing it successfully without having to rebuild the whole environment.
The result is that the Security server performs better now than it has in a while with a number of problems cleared up and I documented the whole process to add to our DRP kit as an optional solution in the event of a disaster.