You're going to run into issues a lot of issues - everything from the lack of 3d acceleration support, to network issues.
If you're trying to have multiple itunes running on the same machine at the same time, you're definitely going to have issues with IP/library conflicts.
Keep in mind that you cannot safely connect an iOS device to multiple iTunes libraries - there are hacks, but they tend to result in wiped devices.
Why not just opt-click to launch itunes and have multiple libraries on the host?