64 bit Windows runs 32 bit programs(like RocketDock) under Windows On Windows emulator(WOW.) To avoid conflicts some redirection is done with registry entries and folder trees. That's why 32 bit programs are installed in Program Files (x86) instead of Program Files. Try installing a 64 bit program in a neutral folder like C:\Utils\AppName, then put the shortcut in RocketDock and see if that works. I have RocketDock on 64 bit Vista. I don't have that many native 64 bit apps. But I didn't notice any problems. Rather than copying any shortcuts from the Start menu, I made my own inside a folder with categorized subfolders. This folder I call Apps. I just dragged the subfolders onto RocketDock.
Here's a screen shot of my Apps folder contents