MSB can encounter problems from time to time, as it has to deal with unknown quantities such as bad/incomplete backups, undocumented format changes imposed by iTunes, mysterious backup files created by the multiplicity of App Store software or files with weird permissions.
In later versions of 2.0 (and higher), MSB tries to provide as much info as it can in the form of a Log.
Send me the log and I can probably determine what the problem is by looking at the last file MSB was trying to access. You can try reading the log and moving the last-named file out and try again. Very often, the file is an relatively inconsequential image or preference file from a third-party app. If you determine that the file is causing a problem, and can attach it, I’d really appreciate it. I’m always looking for ways to catch these problems.