3.
Dear Mr. Krishan,
No difference needs to be spotted in Para 3.06 & Appendix 3B of MEIS.
Have a look at DGFT Notification No. 08/2015 dated 04.06.2016, highlighted below phrase has been added to, which addresses to your concern.
(xvi) Export of milk and milk products, unless specifically notified in Appendix 3B
Also please note that even if the MEIS rate is defined in Appendix for a particular product, DGFT can issue Public Notice thus adding the product under ineligible categories in Para 3.06 and the same will prevail over Appendix.
Further ITC code has to be read as per Indian Tariff Act and MEIS Appendix has been aligned to same. You may take up with DGFT Hqrs for correction of any ITC if the same is not in aligned.