Some have seen warning that file cannot be opened because it has more than 1000 individuals, but only when double clicking a file while GEDitCOM II is not running. I think I found the problem and will post a fix very soon.
In the meantime two fixes are
1. Start GEDitCOM Ii first and then open the file
2. If you get the warning, dismiss it and either double click on file again or use File->Open menu command.
John Nairn