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I applied on 7/10/2013 and fee was taken on 30 of the same month. I received acknowledgement letter with an NFEE reference number. Its been 3 weeks since they debited the fee but when i rang them today with the reference number, the lady told me that that reference number is bringing up some one else's details and not mine. I have checked many times and reference number is correct

All i have been told to just wait which is a bit ridicules.

Is it normal practice to issue acknowledgement letter without putting the application on the system ?

Any input would be much appreciated.

Don't worry, If acknowledgement letter is showing your name and address on it then you are fine. Just wait for your approval. Good luck and God bless you.