I assume that too, but it is nothing special with MY vlcrc since it occurs only when using vlc 3.0.0 and estimated since the time when vlc 2.2.4 was released.
just to clarify: When i delete vlcrc and then reboot gui first start of the gui is fast, creating a new vlcrc and asking for the 2 checkboxes update etc. After next reboot gui is slow again.
So i think something changed in 3.0.0 regarding the vlcrc that causes a "pull the brake" effect on 2nd startup even after a new vlcrc is created.
BTW: plugins.dat is always untouched after once being created with running vlc-cache-gen.exe <pathtovlc>\plugins. it keeps the installation date.