The problem is exponentially greater when you attempt to merge two entirely different cultures. The first challenge is to decide what kind of culture you want to create. This isn't as simple as it sounds. The implied assumption is that the goal of a merger is to select and apply best practices. But that's not always the case.
Companies have comfort zones just as much as people do.
An acquiring company could gravitate toward the culture it is most comfortable with. Or it could adopt the practices that have worked to enhance value in the past. One company may be very open and transparent. The other may be very hierarchical and keep a tight control on the flow of information. And if I asked for a show of hands today which you thought was the better approach, I'd bet that the first model would win in a landslide.