There are times when your website's filesystem permissions get screwed. There's no other way to put it -- some directories are not writeable, some are not ... ARGH! The worst part is that you need to apply different permissions on files and directories, to prevent security issues.
For all (well most) of your console compressing / uncompressing needs, tar is there. All you need to do is set it to work.
Assuming you've spend anything more than an hour with a Linux server on the developer/admin side of things, you've most likely bumped into the filesystem permission scheme.