You know, I think a lot of this conflict comes from the fact that the Slavs, and even more so the Balts, have to assert themselves as nations on the European and even World stage. The Germans and the French don't have problems, nor do the Spanish and Portuguese, since they have been independent nations on the modern era for much longer. They have found their respective positions and now feel more or less comfortable in them. Like to colleagues who have known each other for some time, they can just read each other and this allows for greater trust. The Slavs and Balts, for obvious reasons, have yet to fully develop their own relations. Things are going good overall, I'd say, but bumps in the road are inevitable.
Lithuania also feel threatened, probably, since they are 3.3 million people while Poland is 38 million. And most Poles in Lithuania live around the capital, Vilnius. So for Lithuanians, some perceived Polonization of their main city (which was in Poland until 1939), is stressful. Also, historically, many influential Lithuanians voluntarily Polonized and were effectively Poles in their professional life, e.g Adam Mickiewicz. Statues of Mickiewicz in Lithuania spell his name in their orthography, for one.
We'll see how this goes.