Hi Gregg,
As the 31mm Limited is famous for being sharp even at f/1.8 it should be much better than the DA* 16-50mm at f/2.8.
My advice to you is to find someone in your area who has the 31mm Made in Japan and do a comparison test to see if you have a bad copy.
I've never seen or heard a complain from someone who owns the FA 31mm Limited that is Made in Japan, but I had experienced two 31mm Limited lenses Assembled in Vietnam and they were both substandard to say the least. And I believe there are other people as well who bought the Vietnam version and question it's quality.
Just to show you the difference I found between the lenses see the full size images bellow:
Both shots are focused just under the "NO SMOKING" sign and both are shot at f/1.8.
Made in Japan:
http://farm3.static.flickr.com/2719/4162868642_ac89ebf3f0_o.jpg
Assembled in Vietnam:
http://farm3.static.flickr.com/2691/4162111759_4cbc1ccea7_o.jpg
The problem is definitely not a back or front focusing, to me it looks more like decentered lens.