I haven't observed direct stigma against Eastern European schools, but the big indirect problem may be that US academics are not familiar with your school
When viewing large numbers of applicants or correspondents, this makes it hard to categorize things. Rightly or wrongly, there is often a need to filter more individuals than you have the ability to research in depth, so that can count against you. Note that this isn't restricted to one direction; I lived in Eastern Europe for years, and I had a friend who went to the US to study at Brown. Now, she was in the private sector, but was routinely frustrated that no one in her country had heard of her school, and therefore didn't place much weight on her educational achievements relative to how an Ivy League education would be assessed in the US.
This is similar to the impact of studying at a respected, but small, regional school. There are many of them around the US, and within that school's geographic region you're likely to be interacting with people who are familiar with the school, or possibly even went there themselves. But in a different part of the US, the name of your school would impart no real information to the observer.
Similarly, publications may be in a language US academics can't read, or may be poorly translated, or may be published in journals they've never heard of. In my experience it's very likely that academics will be inclined to judge you, your work, and your program, on their merits once you get past that initial filter. So if your goal is to work in the US, try to build personal contacts with academics in the US (e.g. at conferences, via email), try to publish in English, attend a school with some international recognition (in Prague, for example, you have CERGE-EI which is deliberately US-styled), and anything else that helps overcome that initial "I don't recognize any of this" when someone in the US reads your CV.
