I had the same problem just now. I looked for Hidden Layers as suggested above and also tried replacing the preferences as outlined in the Adobe Forums about this issue, but had no luck. However, I did find a solution that seemed to work … as long as you still have a previous version of ID on your system: I “saved down” the file (from CS5.5, exported as an .idml file) then opened the .idml file in CS4 and was able to successfully package the file from there. Hope this helps.