Since non of us really knows what the situation is likely to be (with the exception of Aviatrix, who cites the German Embassy's site), here's the only way to go around any potential problem in Europe:

1) Go through passport control in AMS: they never ask for a boarding pass when entering The Netherlands and, as a US citizen, the OP is anyway allowed to legally enter the Schengen area without a visa.

2) Walk around to the Schengen boarding area (5-10 min.); they'll ask for your BP (and perhaps your passport to verify it's really you), but nobody cares about your visa condition or whatever is printed on your BP.

Once in Germany, proceed according to what was told you by your University: they certainly know better than us. Only one caveat, it will not solve any problem with narrow-minded DL agents while boarding in the US. This procedure may sound "Greek", but it is a perfectly legal thing to do.