My choice was to give up on Ubuntu and go for Debian, Ubutu gave me a taste of the Debian-style distro, but lacks packages I wanted. (Still have a soft spot for Slackware though) It was not due to a problem like yours however..
When compiling stuff, I usually do as root,thus avoiding any such permission problem. In the Ubuntu universe this takes a bit of finagling since by default you are 'supposed' to only use sudo to execute root commands because actually logging in as root is supposed to be 'bad' in some way.
I don't know if Ubuntu has a pd package but Debian does, http://packages.debian.org/stable/sound/puredata
and I believe the maintainer of the package is on this list too. You may be able to install in on your Ubuntu if the dependencies are met. It's probably worth a try , even if it doesn't work it may provide further information on what the problem is! Any Ubutu experts here care to elaborate ?
I think it's basically vanilla, and you still need to install the externals that you want. But that's not so hard .