I have been looking at QR Codes for a while now and think they are starting to make their way into the market in the UK (supermarket retailer Waitrose is using them in their Christmas advert campaign this year) and into the classroom.
While the MS versions give better control and 'style' than the 'boring' black-and-white QR Code the fear is, and I agree with you in your post above, that people will not recognise the MS version if they see it. This is not the case for the QR Code version.
With hope the MS version will soon drop off the radar if enough of us use the alternative and write it up as the clearer and more dynamic system.
All the best, David.