no, there will not be any problems, but you will be wasteing a lot of money.  I think the east pass costs about $250, German border – Krakow – Prague – German border should cost about $100 if you buy p2p tickets.  You can get your Krakow ticket at the border stop, or you can probably get it in berlin from someone that speaks good english (just show your pass for the German portion of the trip). 

Rob is right, a European East pass is a huge waste of money for this Itinerary.  

thanks for the info… would you make overnight trips out of any of the below?

also, accounting for travel time, do you think this is an okay itinerary for 20 days (june 11th-30th)

fly into dusseldorf — leave asap (got a great price on this ticket, and plan to head immediately to amsterdam)
amsterdam — 2-4 nights
berlin — 1-2 nights
krakow — 2-4 nights
prague — 2-4 nights
munich — 1-2 nights
rome— 2-3 nights
back to dusseldorf

thanks

Berlin-Krakow, Munich-Rome and Rome-Dusseldorf are all reasonable overnight train trips.  However, I’d look for cheap flights first.  Three overnight train trips in 3 weeks would be the absolute maximum for me.

i’ve heard bad things about overnight trains going into both poland and italy, but i’m open for anything—will definitely look into it. i asked this on another thread, but what about stopping somewhere between rome and dusseldorf? think i have enough time for a brief stop in the alps? thanks again

Its not very mountainous, but Verona is a beautiful, small city at the bottom of the Alps.  Otherwise, you can pass through Switzerland, lots of choices there. 
 
If you dropped Rome from the trip things would work a lot smoother.  I realize its probably a “must-see,” but you are traveling almost 1/2 way across the continent for it.  There is always next time.