Was the automation on a plug-in that you later removed from the Master buss? If so, the automation envelope could be orphaned. In that case, try this:
1. Create another Master buss.
2. Drag the plug-ins from the one you currently use to the new one.
3. Map the new Master buss to your output hardware.
4. Map tracks/busses that route to the Master buss to now point to the new one.
5. Delete the old Master buss.