So this problem has been going on for a while now and it's very irritating. It's proving to be very difficult to track down the cause and I'm not sure what to do about it.
First of all, system specs:
CPU: Q6600 4 cores @ 2.4GHz
RAM: 8GB DDR2
GPU: GTX 760
AUDIO: Creative Labs X-Fi PCI Soundcard (Using stereo output only)
Media sources: SATA SSD, SATA 7200rpm HDD
OS: Windows 7 64-bit Ultimate
Current VLC version: 2.2.8 Weatherwax (Just updated from 2.2.6 Umbrella on which the same problem also occurred. Also deleted preferences and cache during the installation.)
The worst culprit for this kind of problem seems to be DVD ISO files which I've copied from DVDs I own to my computer, but it can occur on anything, such as an MP4.
Also, it doesn't always happen, even on the same files. The problem can go away and reappear without any apparent reason.
It's not linked to resources (plenty of RAM free, low CPU usage on all cores).
You'll be watching a video and every 5 seconds or so, the sound will start cutting out for about 0.5 seconds. When the problem exists, restarting VLC does not help.
I figured it may've been a caching, video codec or audio device problem, and I've tried playing with these settings in all kinds of ways: I've seen the problem on different video types, I've tried changing the default audio output device, increasing or decreasing caching values (of all kinds), restarting VLC after each change...sometimes I can extend or shorten the length of the pause (0.5 -> 1.5 seconds for instance), but I can't eliminate it.
The computer has no other problems with any other software or video players. It only occurs on VLC. MPC for instance is consistently reliable and fault free (but unfortunately that video player has less features and can't handle some DVD menus).