My D40 also came from Musician's Friend. I had problems with buttons disappearing into the endblocks within weeks (of course, I played the thing as close to 24 hours a day as I could manage ). I emailed Hohner to get replacement grommets, which they sent for free. I have used most of them and now I'm waiting for my local hobby shop to get the right size of Aerotrend tubing so I can make all new ones.
I also found that there were some unresponsive notes, and that different ranges required different amouts of wind, so that you really couldn't play the extremes of the instrument at the same time. Also, some notes were so badly out of tune as to be humorous. I finally gave in and tried tuning a few of the most offensive - the low C being the worst (it was more of a "B+") - and although I probably didn't do it correctly, at least it made the note useable.
I understand the price difference between a Hohner from MF and a Hohner from Button Box. I appreciate that there is a real need for tuning and regulation in off-the-shelf Hohners.
Cosmetically, my instrument had none of the problems you described, in fact it is quite pretty.
In defense of MF, the price was what caught my eye (I had a gift certificate to spend) and had it been $300 instead, I wouldn't have picked one up, and thus I wouldn't be hooked on the concertina today . . .