Pardon my butt-in guys, the topic sounds interesting so I thought I might chime in too.
CWD The setting you mention in your first post 'magazine' - that's also called other things in different software. You might have a button for 'half tone' or printed page or something like that.
Whatever software came with your scanner, i wouldn't use magazine or halftone. It is meant to be used when scanning FROM a magazine, or any source material that was printed in a dot pattern, and consequently it isn't very useful for any other occasions. I wouldn't expect something like decals to need it.
About the results of your scans. - In keeping with the talk of magnifying glasses etc, it is quite likely that this is what is happening with your scans, with the higher dpi settings in use (800dpi) it's just like using a mag-glass, in other words, if the decal has ANY blemishes at all, then the scan will only increase them as well as everything else that is there.
It's very likely that, at 1/72nd the decals themselves aren't going to be the cleanest, no matter how good the company that makes them is, y'know? you can only get so much out of a printing press at that scale.
So, as adlabs6 mentions above, I think it comes down to the size of the original. If you CAN get 1/48 or 1/32nd scale decals, you're practically guaranteed a better result, using the methods you already use.
Good luck
DeanH