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Hello, this is a very good update. I experienced similar thing when i travelled to Spain with my PR Card and Refugee Traveling Document. Now that I am a Citizen it is likely it happens again but will definitely contact CIC or My MP if it repeats itself. Pls, during your refugee claimant was it your home country you were fleeing from? If YES, that means you got your home country visa on your Canadian Passport. Lastly, did you encounter any questioning on why you visited your country? I am asking these question because I intend traveling to my home country once I get my Canadian Passport. I came to Canada as a refugee too. Thanks as I await your reply.
 
I've been called from the office by the same gentleman yesterday (caller id shows GOUV CAN) He yold me he contacted IT/software drpt and flag will be dropped within weeks. He also reminded if it is not fixed on your next travel after 3 months, i should see my mpp. I will visit NY just to see the result.

He said this is a common issue and happens randomly.

I will update here after my visit to NY. See you guys in 3 months.
please update us if you have traveled