Doubt its a windows issue because I've bound those keys in other games, even other fighting games. Just a game specific issue, like maybe its hard coded to do something in skullgirls but I don't know what.
Numpad is a worse alternative because the 2x3 playing space has other keys around that are exactly the same, if you're terrible (like me) you might end up resettling your fingers over 456, thinking they are 123, then you either get a punch when you want a kick or get nothing at all or your macros.
The other 6 keys are by themselves so you don't have that problem, you can also just slam down your index/middle/ring finger to get both light/medium/heavy buttons without worrying about hitting anything else.
Some solutions (you could use 1 or 2 for the left shift key zeknife if the drawbacks don't bother you) would be
1 - Use a program to switch the binding of a key. This would let you press the delete button and have it function as a different key so skullgirls lets you bind it. The downside here is that all these programs (as far as I know) do this globally, not on a per application basis, and require a restart to work. So now you're stuck with either no delete key for ctrl+alt+del during general computer use or your delete key is in some weird place on the keyboard. Unless of course you want to restart your computer every time you start/stop playing skullgirls...
2 - Write a autohotkey program to change button presses whenever skullgirls is the active window. The downside here is you have to write the program (which would take a lot longer than it needs to if you aren't that good at programming...) and there might be a delay executing your commands as you've added an extra layer of communication.
3 - The keyboard layout creator microsoft has was a potential solution but as far as I can see it only lets you edit a limited section of keys that don't cover where the "delete" and "end" key are anyway.
Was just hoping the game wouldn't be as restrictive as it seems to be, seems pretty unnecessary/lazy, oh well.