As per Section 234A, interest is chargeable for on late filing of Income Tax Return. This interest is charged on Total Tax Liability as reduced by TDS/ TCS, Advance tax, any relief u/s 90 & 90A, any deduction allowed u/s 91 and tax credit allowed under section 115JAA and 115JD.
Since self assessment tax is not mentioned in above, interest was being calculated on self assessment tax paid by assessee before due date of filing of ITR.

Now, vide circular 2/2015 dt. 10th Feb-15, IT dept. has asked its officer not to charge interest on self assessment tax paid before due date of filing of ITR. This decision of IT Dept. is based on the judgement of Supreme Court in the case of CIT vs Prannoy Roy, 309 ITR 231 (2009) where court has held that interest is chargeable after deducting self assessment tax paid before due date of filing.

Complete text of circular can be downloaded from here.