I've never had a problem using one passport here and another one there. You just have to know when to use each one. I've never been to Germany, though.
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I like there and go in and out all the time. I'd say they are thorough but never unpleasant, but with an EU passport it's fairly quick.
One reason for checking carefully could be that with the Schengen Treaty in operation, once you get into one country then you can travel freely to all of the others.