First, about your poms.
- You should not repeatedly add the BioOffice UpdateSite repository to each pom.xml if it is already defined in parent.
- The dependency tag in at.biooffice.rcp_pom.xml is also like unnecessary since Tycho by default relies on dependencies between plugins found in META-INF/MANIFEST.MF
- Similarly, you should define Tycho version only once, in the parent pom. There is also no need to enable tycho build extension over and over again.
With these simplifications you'll see that your poms do not really contain much information, and are therefore not useful for debugging. Besides that, if you are new to Maven, I really encourage you to at least skim through this book to get a better idea about it works:
http://books.sonatype.com/mvnref-book/reference/
Now, about the errors. In my previous e-mail I guessed that your update site is corrupted and asked how it was created. You replied that you've created an update site with Eclipse PDE. Putting these two things together, I think you should recreate it.
Finally, instead of relying on update site created with Eclipse PDE you may want to look into using Tycho target definition files. You can find documentation for them using web search.