We have improved the method we use for generating QR codes - we now generate an image instead of relying on HTML.
It still doesn't look great. Take a look at what I see when I zoom in on my deposit QR code:

The 'pixels' are all different shapes and sizes. Even at 100% zoom it looks rough. The concentric squares in the corners are meant to be symmetrical aren't they?

I wonder if you're using some non-integer pixel size, and we're seeing the effects of anti-aliasing?
Edit: Oh, and thanks for the tip! By rewarding my bug-reporting habit you're only reinforcing it...