Copyright and open source are not mutually exclusive. In fact, most open-source licenses depend on copyright in order to function properly. The GPL comes most readily to mind: you couldn't enforce the requirement to share-alike if copyright didn't let the author decide who may or may not copy the work. But even something as simple as an MIT-style attribution requirement couldn't be enforced without copyright. The Creative Commons licenses also depend on copyright.
Non-copyrighted software does exist (in some jurisdictions). Such software is often said to be in the public domain, and although it is usually classified alongside open-source, it works quite differently: instead of using a license to explicitly allow the sharing of software, it doesn't use a license at all. That's why Creative Commons calls CC0 a dedication instead of a license (though it includes a license for jurisdictions that do not recognize the public domain). SQLite is a famous example of public-domain software, though it does not use CC0.
The "All rights reserved" by rPath is a bit strange to see in an open-source product, but it is probably just standard boilerplate. The GPL renders it pretty much moot anyway; the rights are reserved, but then the GPL explicitly re-grants the rights that make the software open-source.