It appears that with version 6.4 the registry location for 64 Bit machines was moved from "HKLM\SOFTWARE\Wow6432Node\Red Gate\SQL Backup" to "HKLM\SOFTWARE\Red Gate\SQL Backup". While most of the keys were automatically copied to the new location running the SQBServerSetup.exe in silent mode, the datapath key was not. It instead defaulted to the C: path instead of the shared drive path that I use on the PolyServe clusters.
After burning a few hours, I was able to resolve this, so this post it to just confirm the issue, and make you aware that the datapath gets reset on installation. That in turn messed up log shipping.