RECTIFICATION RETURN TDS MISMATCH IN 26AS AND ITR

Dear Sir,

My ITR has been processed U/s 143(1).

However, my TDS as per Form 26AS has not been considered by IT Dept. and now i want to file Rectification Request and Upload new XML.

In new XML, i choose the option as "Filing u/s 139(1) on or before due date". However the system is calculation Late fees U/s 234F Rs. 1000. Also there is no option in ITR to choose RETURN TYPE as Rectification Return.

Now what to do ? 

Please help.