What function are you running to pop the customer alert? Editing the customer? Editing an order for the customer? Also, which program are you running the function, as that might possibly make a difference.

If an OE document, then alerts are also stored on ship-to address codes and perhaps you have alerts set up there that also need to be removed.

We have not heard of alerts appearing for customers for which the records were deleted. Especially the same alert 3 times. I wonder if the data integrity is clean.