I just tried it again. Exporting the data (which is how I did it before) changing some data in the export and then importing the .csv file back into the Ledger. It runs as if it has imported correctly and verifies the import, letting me know how many records were imported and yet when I check the budget data, all records are zero.

I have tried clearing all data (which is why my budget data is zero) and then importing as well as adding some budgets in manually, exporting that and then importing (just to test it), no matter how I try, it won't overwrite what is already there.

I am also using Ledger 9.0B (090713).