I thought it´s now a good time to backup my projects on a DVD with Nero5

But i ran into 2 problems.

first one is that Nero reports that some files are located to depth in folders (to many folders in folders) wich arn´t ISO whatever compatible.

Before Diet Dr. Pepper happenes i turned ISO compatibility off.
Next...Diet Dr. Pepper happens...
After burning i noticed that Nero changed some names of files
Example: It converted:
bes1_bldg_gas_platform.msh.option into bes1_bldg_gas_platformmsh.option (notice the missing dot before msh)

Any Nero experts here who can tell me how to setup nero so it creates a working backup for me?

I think Nero has considered your Mesh Files (*.MSH) as possible virus-infected files because they have several extensions (*.msh.option). Indeed, this is a manner employed by unwanted threats to deceive a user, which thinks that a *.JPG is harmless while it has an hidden extension.(*.PIF, *.SCR, etc...)
Next, to create an ISO image, you must place its main folder at the Hard Drive's root. Moreover, try not to name its sub-folders with spaces and more than 8 characters.
That's all for explanations... Now, if I were you, I'd compress all my files in a *.ZIP archive, which would be burned on DVD...