Though he made a valiant effort, it seems that jdobbs has stepped back from using FFVideoSource as the default frame server in BD Rebuilder. The latest version, 0.48.04, has removed FFVideoSource entirely from the package.
The whole point was to be less dependent on Haali, ffdshow and the DirectshowSource filter, but FFVideoSource was becoming more and more of a problem, especially for Windows versions before Windows 7.
The internal X264 LAV filters remain an option.
If you've been having some issues with the program over the last month or so, this latest version should be a major move back to stability.