Problem with quotation marks

It may not be clear from  @Willi Adelberger 's response, but the language is an attribute that is assigned at the character level.  Dictionary language settings affect only which dictionary is used, when more than one is available, for hyphenation and spell checking for each language and has no effect on the language actually assigned to the text.

If you have "Use Typographer's Quotes" turned on in preferences, InDesign will process a "dumb quote" (i.e the inch marks) to “smart quote” based on the language assigned to the paragraph, whether it's typed or sometimes when it's pasted. If you use the actual key command for a proper quotation mark (e.g. Opt-[ for a “, Shft-Opt-[ for a ”, Opt-\ for a «, and Shft-Opt-\ for a ») will make sure your get what you want. Use these in your Find and Replace if you want to change them that way.

You have to cnange the quotation marks in the correct language. If you work in German 2006 they must be changed there.

If no document is open, the change in the preferences is valid for all new documents, but not for existing documents.

If a document is open, the chage is valid for the current document but not for others.

You have also to take care that the language on the paragraph style is the correct language, and that it is not overwritten with a character style or with a manually setting.

When you choose in preferences set the dictinary to Duden, others  have many bugs in German.

Be aware that Swiss German uses the French quaotation marks, so take care that you use German and Austrian German and not Swiss German.