More likely than not that there is a note about your visit. Depending on the outcome of the visit they may not have noted what their diagnosis was and it may just be ignored by another store. I took my first gen 06 MB to one apple store for a Bluetooth problem and another store a few weeks later for the same issue. There was no mention or question about my earlier visit to another store.
I do this all the time. If I don't get the answer I want at the apple store I will just explain the situation to someone else, until I get a better result. Apple prides itself in providing the best customer experience around...but there are some crappy employees in every company! If you still don't get a good experience, than call corporate office. They will make sure you are happy.