Weird...
I've had no problems with WHDLoad whatsoever. Only issues I've come across is that some of the installers are not that great written... last time I tried Dune for example, the screen flickered and the image of the disk when loading appeared and the music stopped for a second... this doesn't happen when I install the game directly from the floppies without using the WHDLoad installer. Actually, the only game I haven't got to run properly yet is UFO. It flickers and behaves strange, first time saving is always risky because it even manages to hang the computer at times (never happened before in any of the other installs I've tried out). Though, I must admit that I haven't installed that many games, but still... 99% of the time WHDLoad behaves just as I want it to, as long as I remember to run stopnet before, that is... =)
But, what do you mean with "run the games unarchived"?