Hello. VLC is my general all purpose media player.
I recently took a file that has many audio tracks, which plays perfectly in VLC, and removed about 10 audio tracks and then inserted 3 new correct tracks via MKVToolNix.
After the new file is complete VLC can play the file fine but if I try to fast forward at a high speed or jump anywhere in the file more than a minute or two at a time the file will either not play or take a very long time to begin playing again.
This does not happen with the same file in PotPlayer or XBMC.
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Thread: Lag in VLC after muxing
As long as the current version doesn't cause problems with any standalone/hardware players you might be using, which it shouldn't.... software will be updated sooner or later, and as far as I know it's only VLC which has problems because it doesn't follow the rules for MKV quite as exactly as it should.
If you do go back to an older version (I think 5.9.0 would be fine) just make sure you go into it's options and check the "disable header removal compression" box if it's not already checked, or that'll probably give you grief sometime down the line. The setting has been removed in version 6 as MKVMergeGUI no longer uses header removal compression. Thankfully.....