VLC may not remember the playback position of all files and starts at the beginning.
You might try the Moments' Tracker VLC add-on:
Moments' Tracker allows you to track all your favorite movie/media
moments and scenes. Bookmark your favorite moment, give it a
title/caption, and that's it.
Once you've done this, you can jump directly to your moment anytime
you open that media file, no need to scroll through trying to find
certain moment.
If you just want to mark your position so that you could resume from
where you stopped, you could use the "Checkpoint" feature.
Click the "Checkpoint!" button, and retrieve it whenever you want
using "Retrieve Checkpoint" button.
Whenever you open a media file, all your bookmarked moments are
displayed so that you can manipulate it.
Caveat: I haven't tested it yet.
Drawback:
Unfortunately you have to remember to manually save your last play location, but I'm not sure if there's a way around that with the current LUA APIs.
Source Moments' Tracker - addons.videolan.org