It would be very surprising if this were related to Little Snitch. But you could try opening the Little Snitch preferences to see if turning off "show status in menu bar" changes anything. That would prevent it from frequently rendering status updates.
How certain are you that Little Snitch is the only difference between the accounts? For example, is there any possibility that the VLC preferences are different between the two accounts? Some VLC defaults have changed over time. If one account first ran VLC on a different version than the other then the two accounts' VLC preferences may have different rendering behaviors. To help rule this out, you can exit VLC and then erase these so VLC has all default options when you next launch it:
* ~Library/Application Support/org.videolan.vlc
* ~Library/Saved Application State/org.videolan.vlc.savedState