Thanks for your suggestion
I did the same as suggested by you.But apparently it didn't work.
what i observed is with out wazapp also my n9 messaging is having some issue. Today i sent a message using skype, but unfortunately it is showing blank in the conversion and when i move back it is present with different contact name(GSM contact name and it starts with 'S'). I deleted that message and again sent a message using skype, the same issue happened as above, but this time it is moved to the another contact name starts with 'P'

EDIT: I am facing this issue after reflashing only. I bought it from ebay and the seller is from hongkong. I used NSS suite to check the PRODUCT code , unfortunately it is different from the one on the sim tray. I used navifirm and came to know that the product on the sim tray matches with china variant white 64gb version. Due to corrupt installation of nitroid i reflashed it with the Asia/Europe(except china) version 005.