Wow, how difficult can this be.. So you set up nice groups on your old farm and everything worked 100%, now you are creating a new farm and migrated some content, but the site groups did not get carried over.
Well, if you are in this situation, like I am, and you would love all your old groups back, simply download Xavor. You can use the:
stsadm -o gl-copylistsecurity -sourceurl "http://intranet/documents/forms/allitems.aspx" -targeturl "http://intranet/testweb1/documents/forms/allitems.aspx"–includeitemsecurity
but I have a real easy disposition to 3rd party tools, especially free ones.
So I simply copied 1 list with 4 items to the new farm using Xavor and selected on advanced options to export security and import it on the other side.. Tada, everything copied perfect.
Well assuming that you are syncing to the same AD and all that it should work fine.. for me it did.