I have "Build automatically" disabled due to the poor compiling performance of FB (my project has hundreds of classes), and have instead attached a key binding to "Build project" to trigger a build manually.
Unfortunately this option is very often not available, although I have made changes in the project (and saved them).
Yet right-clicking the project, and selecting "Build project" does a build then.
Obviously there is a bug detecting when a build is required or not.
Build project is disabled if you have no project selected in the package explorer/navigator.
Unfortunately, the logic for detecting the project associated with what objecthas focus is not implemented well in Eclipse (see https://bugs.eclipse.org/bugs/show_bug.cgi?id=201650)
That means that if you go to Problems view or switch between editors in a certain way, Build Project gets disabled.
The short of it, it is an Eclipse bug and has been fixed for 3.6 (which is what the next version of Builder ships with).