We mentioned the problem of distributing the Linux version as a ZIP file in previous posts, loosing ownerships and file permissions is a problem when you install the SDK or NDK in a multiuser environment.
Well, we are halfway there, still there's some permission problems that you can fix using android-fixperms that can be downloaded from this site.
Use it like this, for example to change the SDK installed at /opt/android-sdk-linux_x86-1.6_r1
$ android-fixperms --sdk --sdk-dir=/opt/android-sdk-linux_x86-1.6_r1
Hope this helps.