Found the issue.
RipBot264 uses MP4Box to wrap up the video and audio streams into a MP4 container. MP4Box uses variable -IPOD in the job1_MuxFiles.cmd file to add the uuid atom for iPod 5.5G models (aka iPod Classic). Unfortunately mp4box is not adding this special atom into the mp4 file. This atom tells iTunes that H.264 video, up to 1.5 Mbps, 640 by 480 pixels videos can be played on iPod 5.5G
Could not get mp4box to work for nothing.
Then I found nicmp4box.exe and it was "tweaked" to import this special atom automatically. nicmp4box.exe works great. It wraps up my video and audio into an mp4 container and will sync from iTunes to my iPod.
nicmp4box.exe