Captivate was never in the Creative suite, you mention CS6? Which version do you have of CP6? There were 3 versions.
I am answering because I read 'we have hundreds of variables...'. Really! Is that necessary, I'm not astonished that the file gets corrupted at all. I have been developing so much with advanced actions and variables, but always try to lmit their number which is mostly perfectly possible by reusing variables. Of course it becomes easier in CP7/8 with shared actions. Sorry, since you tried out everything that Michael proposes, cannot help you out. Just wanted to transmit this warning.