I can't speak with absolute authority, but based on my own experience with purchasing a firearm and then running into an issue obtaining my CCL initially, I would conjecture that WI gun shops/FFLs run a background check for handguns using the WI Handgun Hotline, whereas the DoJ when conducting a background check uses the Federal NICS database.
I had no trouble buying a handgun, yet was denied my CCL initially. It turned out I had an outstanding warrant from 1998 (failure to pay a fine) in another state. How would I have passed the FFL's background check yet failed the DoJ's check? What I posit above is the only thing that makes sense to me.
Originally Posted by WI Handgun Hotline Website