Unable to open files in InCopy6, etc.

Question

We have been using an InDesign/InCopy workflow for a little over a year. Until recently, we were using InDesign5 and InCopy 5.5, and we had no problems opening and working in the assignments. In the last month or two, some of our new freelancers purchased InCopy6, and it quickly became apparent that it was not compatible with files created in InDesign5. They were unable to open packages, or if a package could be opened it ultimately crashed and lost the changes.
We have upgraded across the board: designers all have InDesign6, and editors/copy editors have InCopy6. However, this upgrade has not resolved the problems and, in fact, the problems seem to be increasing. Many of the files still cannot be opened (often, InCopy shuts down when trying to open a file and says "a serious error was detected"); this seems to be happening more with larger files. Also, some projects open but have pages missing from story/galley view.
Our designers say that they are continuing to work and create assignment packages as before, and even our veteran editors and copy editors are having issues. Does anyone have insight into what may be happening and how we can resolve it? At this point, it's getting hard to rely on this workflow.

Answer 1

Here's a follow up.
I've isolated the issue to a corrupt .indd file. I can't explain how the file got corrupt, but I'm fairly sure this is the cause of my issues here.
Here's what happened.
We use a Dropbox workflow.
I start by creating templates for what we call "program guides." I believe I originally created the template in question with InDesign CS5, but it may have been created with the pre-updated version of InDesign CS6. I don't remember. I then save the stories to a stories folder in the root folder of the document so a compliance officer can edit the content via InCopy CS6.
When a client needs a Program Guide, I then open that template and re-save it into a client specific folder. I delete/unlink the stories and re-export new stories into a stories folder located next to the specific client's Program Guide. Program Managers then edit the marketing portion of the Program Guide content via InCopy CS6.
The issue in this case - the Program Manager could not edit the document, nor could he see the "Galley" or "Story" tabs indicating that InCopy could not see any linked stories.
- I tried re-saving the document, deleting and re-exporting the stories; same result
- I tried exporting the document in .IDML so as to "clense" it and eliminate any corruption; same result
- I tried eliminating elements from the document, one by one, to asertain if a corrupt element (image or text box) might be the culprit; same result
- I finally created a new document, with new text frames and cut and paste the "text only" into the new document/text frames - this worked. When I exported the stories, InCopy was able to see and edit them.
As I believe my original work flow was correct, I still regard this a "bug" in InDesign as the issue seems to have something to do with the way InDesign saves/re-saves an InDesign document.
I do believe I have a tempory work-a-round that will allow me to continue using an InCopy workflow until Adobe updates the software.