I've faced the same problem on Dancevalley, two weeks ago. I had a pearl 2004 that ran september 2000 software, Programming shapes mode 2, and after a while the console only remembered the start-position of these shapes (if programmed). I deleted these shapes and rebuilt them, but the pearl acted like a very old woman... she kept on losing her shapes

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Then I tried loading new software, as far as i remember the feb 2004 software, and loaded the show into the desk, but the problem still existed. I took the pearl more time to forget the shapes, but after a while they still dissapeared...
Then I got a spare 2000, provided it with the feb 2004 software, loaded the show, deleted the shapes before running them, rebuilt them, and that was the most stable construction i faced during the show. I have a backup from that show, I can supply it to Avo. If needed, mail me.