John,
It doesn't sound like you have a problem with the task bar item for the calling window being present as long as it can't be accessed while the sub-vi is open. If this is true, its a much easier task than removing or hiding the task bar item (not currently sure how to do this). So, if you just want to make the caller un-accessable while the sub is open, just make the sub-vi a dialog box. Do this by going to VI properties>>windows appearance and select either dialog box or custom where you can set some dialog properties but don't have to set all of them.
Jared