Have you ever looked at setting up your preferences for the player ?
Anyway ... Open VLC player. Click Ctrl-S (or Settings->Preferences) for Preferences Dialog Box.
Have a look in the Audio Options to make whatever setting modifications you want like volume level, equaliser, skins, etc.
The Audio Tree has sub options for Filters, Output Modules, Visualizations.
There is also an Advanced check box option in the Bottom right. Select if needed.
Do necessary modifications in the above & click Save.
Close VLC Player & reopen it again. Check if your setting has been saved.
I think that should resolve your issue.