John,
this may be more common than you think, especially with the chrome parts. When I installed the chrome primary cover on my bike, there was alot of oxidation/residue in the threads. I had to run a thread chaser through brand new threads on the outer primary several times to clean it all out. I would'nt think that a harley factory tech would go throught all of this. I would assume that they stick the screw on an air gun and install the derby cover. This practice probably doesn't help when removing the derby cover for the first time. Sorry for you woes, but it's just a cost of doing business I guess. Make sure that before you reinstall the screws, that you run a thread chaser down the holes. You may be surprised what you get out of them. In my opinion, a thread cleaner set is an essential part of any tool kit, especially when working on harleys.
hope that helped a little.
harry