VoiceAttack would use the exact same API calls as on your previous machine, so it could be something is configured differently in Windows, or an application that wasn't present before is interfering somehow.
You can select multiple commands (or all commands, by pressing Ctrl-A on your keyboard), and click the "Edit" button to open the "Command Multi-Edit" window, which allows you to change the targeting option for your commands.
Though, if you're using the active window, I would leave the "Send command to this target:" option unchecked (while having the "Update" box next to it checked), so that the option is cleared, and the profile-level option is used instead.
Unless a specific command should be sent to a different application than all the other commands in your profile, the "Send command to this target:" option should not be enabled at the command level, and the "Send commands to this target:" option at the profile level should be used instead.
Doing so enables you to change the target for all commands in the profile without having to edit the commands themselves.