phpDocumentor 1.x is php4 code, and so running it on newer versions (especially 5.3+) triggers many such notices and warnings. You can lower your error reporting threshold to hide them, but a better option for newer PHP code is to try phpDocumentor 2.x, which is in beta right now.
As for these notices having a negative effect on the docs you generate using 1.x, your docs should be fine. Those particular notices are not failures of any kind.