Why might it be difficult to make a 64 bit version of a program?

In my short time programming, it has been trivial to compile any of my C++, Java, etc. for either a 32 or 64 bit machine so long as I have the full source for the program.

But a lot of software is not released 64bit. Most annoyingly, there isn't yet a 64bit release of the Unity engine.

What makes it difficult to compile some programs for 64 bit machines?