Unlikely. MA only transfer user files, apps, and any associated files those apps need to run (like Photoshop, which installs things into /Library, and not just your particular user's directory, although it does do that too).
If anything, the only thing you can break are the apps that are being migrated or fail to transfer some of your files (music, documents, etc.).
The Power Saver preference pane is located under /System/ and that is in no way modified by MA. Nothing under the "/System" directory is written to, and that is where the OS (and it's core files) are found (among other places, not openly visible to the end user).
It may be that the settings for Power Saver are corrupted (and those reside in the user's directory, specifically ~/Library/Preferences/).
The best solution, would be to boot using the recovery utility (or safe-mode) and delete the user's directory (e.g., /Users/{your username}) and start migration assistant again once you reboot normally (at which point OS X will take you through the registration process again). Obviously this would delete all the files from that user (music, movies, etc.) so make sure you have backups of everything.
Alternatively, you can log into OS X, create a new administrator account (but don't use your regular naming convention, call it Jonny Appleseed/john, for example) using the System Preference's Users & Groups, log out, and log back in using that new account, and then delete your old administrator account, then recreate it using the same steps you did with the currently logged in account. Once that is done, log out and back in with your newly recreated account, and delete the extra administrator account. This will ensure your new account is set up using the same naming convention your original account was set to (making things easier for MA).
Running MA after that, should transfer all the files over again cleanly without having to worry about somethings getting overwritten or not overwritten.
It is also of note that MA just copies over files and doesn't move them. So all the source files are still there and once you delete the user directory, it'll be a total fresh start.
Yes, i'm the IT Manager for an Ad Agency using mostly Macs, and i've done it all, 10.4-10.7 and it's almost never a problem. Are you using AD or something for authentication? Migrating from 10.4 all the way up to 10.7 has always worked for me.
As a suggestion, try installing Applejack on the system and running it. It's an excellent a ppm, and has sorted out issues for me more than a lot of times.. It's been a lifesaver.. Also, Are you using Firewire? or Ethernet to migrate user accounts? Ethernet is by far the fastest/best way to migrate user accounts between 2 machines
Wow, that was totally wrong. Sorry, i was not paying attention when i wrote that...
EDIT: Firewire 800 is the fastest, Firewire 400 is the next fastest, Ethernet is the slowest, and Wireless is unusable.. Sorry... Msg me if you are still having problems, and I'll try to help!
Best Answer
Since this has failed more than once, it's likely you'll have to effect some repair or change tactics.
Here are a few that seem likely - you'll have to choose based on your specific situation:
Do note, that one possible cause of the freezing could be hard drive failure. If that's the cause, you want to get the important files off first and avoid 'fixing' anything. (Imagine a potential house on fire - you may not have time for everything, so prioritize and just get things out now - organize them later.)
All the other causes are not as dire and you may have time to try things again and again, just wanted to plant the idea that this might be a warning so you could get professional help if there are valuable or irreplaceable files on the freezing computer.