Missile hitbox sizes being broken is a thing in a couple recent nightly builds (that newest MediaVPs require). IMO, just roll back to some less recent one, here's how to do it:
In Knossos, enter the settings menu (gear symbol in topright corner), section "Knossos", mark the "Show builds in mod list" checkbox, change "Preferred engine stability" to Nightlies if it isn't set to that, hit save and enter the Explore tab. Navigate to FSO mod, details, choose an older version in the topleft corner, I'd suggest something dating about a month back (release dates are in the build names), then after selecting it, hit "install" and once it's done, navigate to MediaVPs -> details -> FSO Settings and choose the build you downloaded there.