2) Where is my gff annotation? The space is presence for it but nothing but the scale ruler is visible?! Did you set the reference sequence start index in GATAligner? Pull up the GATAligner Parameters Window from the Alignment menu in GATAPlotter to check. If necessary realign the sequences. Also double check that your annotation file follows the GFF format.
3) Since installing the new GATAPlotter, all my old GATAlignments are whacked! Unfortunately, new releases of GATAPlotter may not be compatible with prior GATAlignments due to updated serialized objects. Re align the sequences using the new GATAligner and throw out the old GATAlignment.