I am not sure what exactly the issue is (without looking into the model). The corners can be treated in some ways (attaching a movie below..if sheet metal operation doesn't work for you then probably this will but it will be good to see your model first if possible).
To me your model looks good. Just one recommendation ...if possible then please modify the dumb BODY feature before Converting to sheet metal.
Find attached the part. Does this makes sense to your case?
As i recommended earlier also..it will be good if you can get rid of these geometric discrepancies in the begining itself (before using CONVERT TO SHEET METAL).It will save you lot of manual effort.
These Catia->NX converted models are horrible