You sent a second tax return? Was it an amended 1040X return? That might part of your troubles. You only file 1 return. If you need to fix it you file an AMENDED 1040X return, but only after the IRS has processed the first return.
Then when you import your forms from the broker, etc. you still need to double check it over. There can be mistakes on the import or missing info. You can't trust it to be right.
