What you are describing sounds more like a ripping issue -- some rippers don't rip properly and thus the transcode has problems.
This thread is so long I'm not even sure where we are at so a recap might be in order:
1) Are you using one of the nightlies version of Handbrake? Not .94, but a far more recent downoad? If not, do so immediately.
2) Are you ripping the full DVD to your hard drive and then encoding from there? Most rippers offer various options to only rip the main movie or some part, but I would not advise this (alternatively, you can directly encode from Handbrake from the original DVD if you have a ripper like AnyDVD installed).
3) Can you post the MediaInfo for one of the problematic files? If it's not ALL files then it may just be a problem with some DVDs. There are some known issues with very esoteric DVDs (like the ones the BBC produces, which do odd things with interlacing and frame rates).
Mainstream movie DVDs should not have any issues with latency encoded with the latest Handbrake to an MKV file and played on a local USB drive (playing network is a whole different ballgame -- if you are playing these via your network you need to post this issue in the network forum) and going striaght to your display.