I don't think this problem has much to do with you being an aspie. When my husband first came to the US from England, he got the same reaction. I think a Scottish accent is generally harder for Americans to understand, but my husband's accent (as well as his choice of words and the way he phrases things) really used to take people aback. It wasn't one of the accents that Americans are used to hearing on television. Waitresses would get all flustered and confused when he asked if they had any savoury pies or clotted cream, or other things that Americans aren't accustomed to.
He's still got a bit of an accent, but it's not as noticeable. After a while, you naturally pick up the speech patterns of people around you.
I think it's something you just have to put up with for a while. When I was in England, I was amazed at the variety of accents, within such a small geographical area. In the US, there are different accents, but not nearly so much. We just aren't used to hearing a lot of it, and it's a novelty to hear something "unusual". (I watch mostly British TV now, so I've gotten accustomed to a wide variety of accents that I didn't used to be able to understand.)
In fact, I remember working at a pizza place, and getting really nervous when a guy came in and started to place an order with an English accent, because I was afraid I would embarrass myself by not understanding him. That was just me being a jittery nutbag.