I don't recall anybody reporting anything like this before, so I don't know the answer. You'll have to do some experiments to figure out the cause.

I would begin with the following tests:

First, I would remove all the toggles from one of the problem hotkeys and see if the problem still occurs. If so, you'll know the problem has nothing to do with toggles but rather has some other cause.

Second, I would change one of the problem hotkeys so it's triggered by a single key press instead of by a key combination. For example, rename <Hotkey Shift X> to <Hotkey F1>. If that elminates the problem, you'll know it has to do with an interaction between HotkeyNet and the sequence of key events that your G15 is sending to the operating system.