I have done all of the steps within your last post previously. I have also tried trashing all profiles and started again using the Wizard to add all characters but to no avail.
Then I don't have enough information to uncover the problem. If you were to show me your config I would verify that the battle.net and WoW account names are set up per Character, and that Config.WTF is virtualized. If you created them with the Quick Setup Wizard and didn't change them after, then it's automatically done. The only other thing I would be looking for is whether or not you have multiple WoW folders.
I did forget one other condition. Your IS profile has to be pointing at wow.exe (not, say, the wow launcher, or some renamed wow.exe). I don't know why it wouldn't be, but just throwing that out there.
Some things I can't really verify, like that the character was logged in, or that WTF\Config.WTF already exists in all of your WoW folders. I also can't really verify that when you close out WoW after launching your guys the first time, and Export, that it doesn't fill in your account names. But at that point, the virtualized Config.WTF should already exist -- so you should be able to go into your WoW\WTF folder, and see a Config.WTF for every single character. If that exists and ISBoxer isn't offering to fill in the account names when you Export, the account names either aren't set up for your Character or you're clicking No when it offers to fix it.
That's really all there is to it. If you still need help, it would help to check these things and tell me what you see -- telling me you "did the steps" doesn't really help and usually when people tell me things like that, they skipped half of them
I don't see how it can be the Key Maps as I do not touch the maps or repeater settings when I remove and then re-add the username & password yet once this has been re-typed it logs me in just fine.
Are you saying you're definitely not turning off Key Maps when you try to log in, and you believe there's no reason to turn them off? You're welcome to log in however it works for you, I guess. There are times when you can type in your password 100% correctly and the game will tell you it's wrong, even without ISBoxer. If you're leaving Key Maps on and you have numbers in your password, or other ISBoxer hotkeys, it's going to alter the entry of your password. When you're typing in your password with broadcasting on, it is a good idea to be a little more deliberate with your password entry than you normally would be
It seems to get confused with specific combinations of the ALT, CTRL, SHIFT & certain Numpad keys?
Shift is not very compatible with the number pad. Shift+Num 1 for example is End. Just avoid using Shift with the numpad keys