Sometimes bank staff are funny like that, but to be honest, they should not complain because after all, they do have YOUR money...
My Mum banks share dividends etc in Abbey, and likes to have each entry separate, not all as one entry. She rarely speaks up for herself, so one time the cashier refused and made a note in the book informing any cashier who deals with my Mum again, not to do them separately.
I had to go in to speak to the manager (just a few minutes later, as I was in another shop), who first argued that he cannot speak to me because I was not the account holder (my Mum was with me), and then pointed out the cashier would have refused because it was near lunch and they are often busy. I pointed out of his glass office to a literally empty branch... and after a few more random points from him, I got him to remove the note, add a new note saying they would process items separately, and then sign it
Always kick up a fuss, because at the end of the day they are getting your custom, and if they have a problem with that, then take it elsewhere