I had this issues and saw several posts with the same problem. I fixed mine with this solution. Hopefully this can help those with the same issue.
Problem: The data from my 1.9 env did not get converted over to moodle 2.0 I got errors that said "file has not been migrated". I had moved my data from the 1.9 to the /data/moodle20/ directory but it didn't get moved to the new directory structure. I know it works since i got it working on my test system first.
The fix is obvious. I made the config ='/data/moodle20' (I have left off my parent directory in this example)
I noticed this first when the upgrade was happening and a bunch of errors occured under the Forum, Wiki and Glossary upgrade areas. They all complained that the "file is unreadable". This did not happen after I made the fix.
Good luck. My moodle upgrade was made much easier with some serious practice on my test system, which I highly recommend.