So far this is what we have figured out. Anything else anyone has come accross would still be appreciated as it doesn't look like a problem that is going away.
The "Repaired" Sheets listed in the "Log" are in literal order and not by actual sheet name when viewed in
VB Editor.
As mentioned, the repairs overwrite the formulas with a hard code value. To find these we select the areas that should only be formulas and then use "Go To Constants" (Ctrl-G > Special > Constants) which isn't very creative but has been helping.
Beyond this we are still lost as to why it happens and how to prevent it.