1) When in Windows, I use the nightly build and set it in D:\Codeblocks, in Ubuntu, I just get your SVN (all by terminal, I'm new to ubuntu so I do not know where it's installed)
2) In Windows, I create a folder D:\C++ and put project named "Project" in that. In ubuntu, I also add project named "Project" in the same place as Win (this is why I think the problem you talked about came from:
Do you share the config-folder ?
Please help me to fix my problem. Your help ís appreciated