Yes, I had a similar problem. Spent a year studying at a school in Florence, and asked for a "transcript exception" based on the fact that it was a foreign school. Unfortunately, the school I attended had some kind of affiliation with a school in Cleveland, and AMCAS assumed I was enrolled there as well. My application was pulled out of verification because of this "missing" Cleveland transcript.
After I explained the situation to AMCAS, they told me I would have to provide a letter from the school in Cleveland saying that I'd never been a student there. The registrar at that school was very sympathetic and faxed something over that very afternoon.
This suggests a possible solution to your problem: ask AMCAS whether, instead of providing a transcript from Stuttgart, you could have your undergrad school fax them a letter stating that what you had attended was indeed a study abroad program. This could save some time.
By the way, if you haven't done so already, get the direct phone number of the person you talk to at AMCAS. This will save you hours of being on hold on their help line.
Good luck! Dealing with AMCAS can be immensely frustrating, but things will work out eventually. Just be persistent.
