Something tells me that you made a rather honest mistake when changing the windows shortcut to do your bidding. And also that you got what you wanted but the deal is only half complete.
A windows shortcut is just a script for running a program with a pretty gui to help you out, and also running a program with command line arguments. Lets say you get onto someones computer and you change the internet explorer shortcut to instead of opening up internet explorer, but instead pull the command for shutting down the computer.
What i'm getting as is what happened on your end with is half complete. It's really sounding like you got rid of the target executable path in the shortcut and just replaced it with the processor affinity commands instead. This would easily get a shortcut to not run your desired program.
A better way is that we'll say -xxx is a command modifier for ascii art boob graphics (just imagine it's like setting the processor affinity commands) all over in your game. So you want boob ascii art in your game. Alright, easy enough. C:\example.exe -xxx there, it's done.
What it sounds like you've done is you unknowingly got rid of C:\example.exe and just left the -xxx part in the shortcut. This would explain why the shortcut is just dumping you at windows command line instead of running the game with the processor affinity in an easy double click solution.
So in by learning that windows shortcuts are just scripts, you now know they can do more than just loading programs, you can just have them run really any kind of command you want. You can change a shortcut just to run dir or cd if you wanted albeit that would really be pointless, but this is where i barely keep myself from ****ing with people's shortcuts. What i do is more genius than making My Computer open calc instead. But, by embedding nasty little commands like hibernate, sleep, restart, or shutdown to a couple of icons on the desktop, you've really convinced somebody they got a virus causing instability
Or you could be really nasty and change a shortcut to delete the contents of my documents and the directories within. I haven't been cruel like this before, haven't met anyone i hated enough to want to do it.
bla bla bla, i hope i helped.