BuddyPress.org

Maybe it isn’t a server issue then but it’s difficult to suggest what else may be the issue. I have updated three separate installs to 1.2.6 recently in production environments and have not experienced this issue.

One thing that I do avoid is ever using the autoupdater as I believe this can cause issues with server permissions and don’t trust it generally, I only transfer updates via FTP.

You might need to contact your server support and ask them if they can check user and group permissions as I mentioned earlier, doing this while checking other possibilities might be wise?