I can export fine with old, duplicated, or brand new events on front end and back end.
I did have a problem on the front end -- not all the events showed up as available for export. I went back and made sure i had selected an event owner and all seems to work fine.
No solutions for you but some suggestions of things to check:
Especially if you've upgraded recently, configuration might need to be saved again
Or, upgrade to 3.1.6f
make sure there are records in both events you're trying to export
make sure permissions are set, and/or re-save them.