Jeff, This is a known issue with a very few BSA uniform shirts. Sometimes suppliers get buttons that do not meet BSA specifications. BSA will replace the shirt for you at no charge. Just take it too a council store or send it to BSA Supply Division (see Scoutstuff.org) and they will take care of it.
The slight discoloration (other than from the buttons) is Badge Magic residue that was not dissolved by the dry cleaning. It is caused by ironing on the badges or ironing over them to heavily. This melts the adhesive into the weave of the fabric. Don't worry, you can get your uniform back into First Class condition!
If you are putting another patch in the same place, you can ignore it and put the new patch on right over the old spot.
If it will show, use a solvent such as Goo Gone or Goof Off to dissolve the residue. This is explained in detail on the Badge Magic website in the FAQ section and there is even a video of the procedure at http://www.badgemagic.com/info_pages/index.cfm?fuseaction=all&parent_id=30.
The short version is to squirt the solvent on the stain and soak it up on the back side with a paper towel. Rubbing will help. Repeat this until the stain is gone. It may take several applications if the badges have been in place awhile.
If you continue to have a problem, the folks at Badge MAgic will help you. Just e-mail them at info@badgemagic.com.
