I got the same problem.
Becouse of the problems with Plesk 10.3.1 on CentOS 5.6 we wanted to move to CentOS 6.0. But like EVERY TIME in the past 10 years the migration is not without a lot of problems.. (Even is we try to do thing like Parallels want them)
After a lot of testing we found a databases were incomplete, missing tables.
We started the migration all over, now the database was nowempty.
No other errors found so far, but there are databases that are empty or incomplete..
Because there were no errors, its very tricky to comfirm the migration has gone ok..
I manually extracted the database sql file from the migration files, it was also empty. I could not find any errors on the target server, and did not find a /migration/ folder on the source server.