If your account is moved between servers, they may have to run custom written scripts to fix / update some file permissions, but this is rare. Do you know if your site has been moved between servers? Not as in one hosting company to another, but between server A and server B of the same hosting company?
For example, if you’re on a server in which the hard drive is getting full, they may migrate several of the accounts to a different server to help with the disk issues. An account may also be moved to a less populated server if that account is using excessive resources, such as CPU time / memory.
Why do you assume you’re having permissions issues? Further details on that would help troubleshoot the issue.