I'm not completely clear on what you're doing, but I think I might be doing something similar. That said, I have no idea how Shared Variables work, so I can't help you with that.
I'm doing it with an action engine that reads from and writes to a file on the hard drive. Since my code involves a "path to current vi" node, the .exe files will only be seeing data on the computer that they're on, and other users with similar programs running will not interfere.
I don't know if that helps you, but that's what I'm doing and it's working fine for me, so I thought I'd share.