The problem you're describing is a known bug. It happens only on faster machines and I'm still researching the problem. It has most likely nothing to do with your aux-keypad.
You might want to try to insert a delay in the text to send and see if that fixes the problem (simply insert the text {DELAY=xxxx} anywher in the text to send, where xxx is the amount of milliseconds to wait). It has been reported to work on some machines and not on others so your mileage may vary.
As to the other highly desired feature: that would require writing a special component that traps those keys. Windows comes with a built-in component that you can use to press a hotkey combination, but that one doesn't accept the Windows key. I'll see what I can do in the next release. At least, I've added your request to the desired features list.