no 1099-Int should have been issued since the interest was earned by the tax-exempt retirement account. as for the k-1 I2 in part II should be checked since the partnership was owned by the retirement account. checking this box tells the IRS the real owner was your retirement account. there is no such box on a 1099-INT
you should contact the custodian to issue a corrected 1099-INT.
if I2 isn't checked a corrected k-1 needs to be issued.
