With antix 8.5, I have a custom, very distinct conky config that's working fine, but whenever I boot/log into Antix, the conky config that loads on startup is the default one.

I can remedy toggling it off then on again, (by right clicking on the desktop and choosing Desktop > Conky On/Off, 2x) but I'd like my custom config to"stick" and be the one that appears automatically on boot.

Open pcmanfm or rox file mamanger. View Hidden files. Look for .conkyrc. Edit it to match your custom conky config you did using Control Center.