If you've waited long enough for a conforming activity, create a new project, bring in a short section of your 5.1 material. Does it preview?
Now bring in your long one. Evidence of conforming? does it work?
My guess, based on Richard's (I think it was Richard) comment in another thread, is that Encore must do something to be able to preview as stereo the 5.1 passthrough file. I also assume given what you needed to do in your project, that Encore may have just lost the preview info, or has become corrupt.