Reasons for conflict between the two personalities
The primary desire of a person with the ENTJ personality type is to be valued as someone who made useful contributions to the world by making it more efficient, resilient, honest, rich or just by getting big things done. Because extroverted thinking governs almost all their actions they may be accused of not being creative enough, or being too focused on the end results. Those accusations usually come from an ENTP whose life revolves around extroverted intuition, or just being unique. A typical ENTJ - ENTP conflict will revolve around statements like "you're just too stubborn" (to the ENTJ), or "you don't know how the real world works" (to the ENTP). An argument between an ENTP and an ENTJ is often a spectacular thing to watch and their flaws can only be obvious to an outsider.
Most conflict between these two personalities happens because ENTJs and ENTPs represent two different spheres of thinking which serve as a sort of critique towards each other. Examples of this can range from an ENTP artist criticizing an ENTJ government to a narrower example of an average ENTJ telling an ENTP that he doesn't have ADD, he's just bored and lazy.
Before the end it should be noted that like all relationships this one is also dictated by many other factors besides personality type. Life circumstances can bring each of these types into a superior position and that obviously changes people's behavior.
ENTPs and ENTJs can be friends and they can be enemies, but one thing is for sure, they can provide each other with a very different way of looking at things, and that may prove valuable in life for both of them.