OK, now I feel a bit stupid.
In the Setup Wizard screenshot above, you'll notice a line that says 'Show Vert/Horiz - Auto Based on Display'
That line is filtering out all games that are Vertical Shooters / Scrollers because of my normal horizontal display, no wonder Space Invaders and Centipede didn't show up, DOH!
I still can't get the Update List to not verify the ROMs, if you check the log it always includes -verifysets, but when I checked the verify.dat file that gets stored in users\'username'\appdata\local\temp and found the missing games in there and listed as GOOD I knew it couldn't be a verification problem.
Well anyway, I've learnt loads, thank you very much to everyone who has helped, much appreciated.
spiffo.