Not sure I understand all of your terminology, is there both inter and intra divisional play? If yes, then I am not aware of any program to help, if not, have you looked at the Excel generator (see the topic at the top of the list in the requests section) which will probably help if you use it in "Home-Away" mode. There is no reason why you couldn't use part of a complete round-robin for a short season or use more than one copy of the round-robin to get teams playing each other twice or more per season.
Ian.
