I just got a temporary workaround for this issue from Microsoft. This is a manual way to do the definition updates, and so you'll have to do it to update definitions each time you want to update them until they release a patch.
- Download the definition updates from Microsoft. https://www.microsoft.com/en-us/wdsi/defenderupdates (Choose the System Center 2012 Endpoint Protection 32 or 64bit based on your OS)
- Extract the downloaded file using 7-zip or another application. This should give you a all the different update files split out.
- Copy all the files to the updates folder "C:\ProgramData\Microsoft\Microsoft Antimalware\Definition Updates\Updates"
- Wait a few minutes and you'll see the files disappear and your client will be updated to the latest definition updates you downloaded.
I was told I would be updated once they release a full fix for the issue. So until then we'll be doing this manually.