You may not be getting a good enough seal the first time. My first few projects were like this but I've found that if I use a brayer and roll it over the paper after gluing it down (before sealing the top layer) that it goes much better. I use modge podge for adhereing the paper to the wood, then brayer a few times, then use whatever sealant over that once it dries. Hope that made sense and it helps!
~Crystal
http://sweetteetle.blogspot.com/