My new 10/22 TD (purchased on May 5th) had the exact same rear sight problem as noted in this thread. I too shipped the TD back to Ruger, and I'm waiting for its return. I'm happy that they fixed the issue properly for the original poster.
After I noticed this issue on my rifle, I went to a local shop which had six 10/22 TD's in stock, and each had the same rear sight alignment issue as mine. I looked at other new 10/22 models (not TD) on the store shelves, and all the rear sights looked properly aligned with the barrel.
I also went to a local Cabela's this past weekend, where the TD is currently on sale, and grabbed a TD off their shelf and looked at the rear sight. That rear sight is also aligned a bit off, though maybe not as bad as mine nor the other six that I previously looked at.
So my conclusion is that the issue has been prevalent on the initial batch of new TDs shipped, and if people are not as picky as I am with a 300 buck purchase or are planning to never use the iron sights in favor of mounting a scope, then we are not going to hear about the problem on this forum nor on other Ruger-related forums (which I've been monitoring for mention about this issue). Ruger has received at least 2 TDs returned for service for this rear sight issue so far.