The slow pace of industrialization, diluted national/cultural identities, and Communism.
Eastern European countries were formed, in the shape we know them today, mostly after the collapse of the Ottoman and Russian empires and the treaty of Versailles following the first world war.
Most of these countries' territories had long been disputed by the great powers in Europe (Austria-Hungary, Russia, the Ottomans), while their inhabitants had few rights, or opportunities, to rise out of the agricultural sustenance in which the majority were living. As a result, there were poles of modernity in some of the capital cities while the rest of the country would be politically and economically isolated.
Industrialization was slow to reach these places, hence the increase in the standards of living associated with countries where industry accelerated the pace of economies and the stagnation in Eastern Europe. Slow, however, does not mean inexistent.
The final nail in the coffin for Eastern European countries were the post WWII communist governments. While the economies of countries like Romania were comparable to Spain or Portugal before the war, communism effectively held back any hope that progress could be made. Communist governments were preoccupied with quotas for products that were often not needed on the market, with ideological education -as opposed to useful education - and with a cold war they had no chance of ever winning.
Once the iron curtain fell, the whole world was able to see how Communism ruined entire countries with poor planning, corrupt practices, and generations of people who were unable to think or create wealth for themselves without resorting to theft or other forms of corruption.
Most of Eastern Europe today is long past the rural, pre industrialized era where large regional powers dictated their fates, but the Communist legacy and mentality is still going strong, as demonstrated by their deeply corrupt and inefficient governments.