This happens when you install mods with SMM while the editor is running. Either don't do that, or use File > Reload Database as soon as you return to the editor.
Updated the FAQ with this question, though I thought I've already done that...
FtDLulz wrote:Drone count does not seem to actually update, it resets itself to 2.
Nice find -- got that fixed.
FtDLulz wrote:Also, when I go ingame, the enemy ship hull is invisible. Thirdly, when setting a enemy ship's weapon list to 'WEAPONS_FREE', it spawns with no weapons. I'm assuming that's because there's only three weapons in the list and the weapon count is 4 for the enemy ship, but I could be wrong.
Edit 3: Just tested with a list with four weapons, still didn't show any. Set it to WEAPONS_JELLY and it worked.
No idea why that is *shrug* I remember there were some issues with enemy hulls, but I've never figured out the cause. Sleeper is much more experienced than I am when it comes to enemy ships, so you may want to ask him instead.