(d) Notwithstanding any other provisions of this article, assessments may be issued only within the following time periods:
- (1) For tax liabilities, if the taxpayer has filed a return for the tax and taxable year at issue, within three years of the filing date for the return or the date upon which the return actually was filed, whichever comes later;
- (2) For fees, within three years of the date prescribed for payment of the fee;
- (3) For penalties based upon a failure to pay a tax, at any time.