hey scott,
ring the ato help line or the person in charge of your case, i have been told but dont hold it to me if a tax practiconer has lodge a form that is not satusfactory he may be eligible for the full amount, you have done the right thing by getting all of your records back, i would be going to a new accountant, and get them to go over the whole thing with a fine tooth comb, then i would lodge a amendment of the previous years tax if you find any discrepencies, as 1 small mistake made by the tax agent can cause thousends of $$$$$ and this can be fixed. if your accountant was at fault due to a error stick it to him for damages and any fines asociated. the people at the ato generaly are good people and cop alot of flack from people due to errors made by accountants and the accountants can be held responsable for the issue. try not to stress and if there is a issue and you do owe money and cannot pay expain why, you may find that your troubles will fade, unfortunatly you may still have to pay the money back but they may be able to deduct it out of this years tax. im feel for you and im sorry i cant help more or give better advice, just hang in there and take it one day at a time and things will work themselfs out.
goodluck pauly