The apeinfo update was mostly to address compatibility issues. It's been updated to properly support GCC 4.x (which almost all Linux distributions ship with today), and I've also included a 64-bit binary for those of you running 64-bit Linux distributions. The older 32-bit still works fine if you'd prefer to use it, but using it on a 64-bit distro will require installation of 32-bit compatibility libraries.
Convert to FLAC received a much more significant update, and has been bumped up to version 2.0 as a result. The highlights include the ability to accept and process multiple input files, support for Apple Lossless (ALAC) and True Audio (TTA) input files, dynamic path setting for "helper" binaries (so you no longer need to edit paths in the script), and a rather import bug fix to ensure that both the decode and encode steps in the transcoding process are completed successfully. Anyone using Convert to FLAC is strongly encouraged to update to this new version.