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Never had this issue myself, but there is a Support doc that describes an issue that looks like the issue as you describe it, perhaps it help you
E-BI/XMLP: The Pie Charts Designed in RTF Template Builder Are Not Retained in PDF Output Report When Using PIA Navigation [ID 827604.1]
Just tried it and right clicking on a chart pops up a menu with the last option of the popup menu being BI Publisher Chart.
Do you have .Net FrameWork 2.0 installed on your workstation?
When your workstation for example runs on Window 7, this has .Net FrameWork 3.5 embedded in the installation. Uninstall .net framework 3.5 and install .net framework 2.0 from the installation dir where you installed BI Publisher Desktop
(default dir) C:\Program Files\Oracle\BI Publisher\BI Publisher Desktop\DotNetInstallFiles
See also a post I wrote a while ago on this subject.