I had a Z1 put in my truck a couple months ago. The other day I was doing working on the stereo system and noticed the manufacturing date listed on the box was Oct 2006, but the manufacturing date listed on the unit was May 2006. I didn't remember to check the serial numbers before I closed it all up though.

Is this common or did I get screwed by the place I bought it/had it installed? What would a reason be for this?

Probably swapped at the place you got it. They may have given you the wrong box, or they may have given you a different deck they had sitting around