I've noticed...

If you press a single key, keyclone reacts as you'd expect.
But if you do a combination then it depends on the order of the keypresses.

If you were to go...

Shift key (down)
W key (down)
W key (up)
Shift key (up)

You get a capital W.

If you release them in a different order:

Shift key (down)
W key (down)
Shift key (up)
W key (up)

You sometimes get unexpected behavior.
But keyclone is working properly because it is broadcasting what you type.

You might have "w" on the do-not-pass list, and not want that to broadcast.
For example "w" is your default move-forward hotkey.. and you'd like your slaves to auto follow not move when your main moves.
So "w" does not pass.

Holding Shift down, might be bound to moving your alts together.
So the first example where its, Shift-down, W-down, W-up, Shift-up moves your alts forward.
But the second example seems to buggy because you're trying to shift-w to move your toons, but keyclone has been told to not pass certain keys.

I've found if I have a wow macro, such as Shift-down, Tilde-down, Tilde-up, Shift-up and press in that order, as in modifier first down and last up, it works great. If the modifier and key follow an alternating sequence like Shift-down, Key-down, Shift-up, key-up, sometimes depending on your configuration you don't get the expected result.
If you take the time to ensure your modifier is first down and last up, whenever you use modifiers you generally receive the expected result.