I'm having this exact issue, I've set up all the crew orbat says each position is filled but in game its only the driver.

Gave up on this awhile ago. But it may be an issue with RHS

It's not just RHS, it's OPTRE too

You need to export CfgPatches.

Having this issue too, even w/ exporting CfgPatches.

i got ways to fix this, but not everytime it works. For what I did, first i export all codes and cfgpatches config to files, and i created a PBO file for the faction mod, then i made a standrad addon folder which can be loaded by arma3. Then i loaded the addon folder i made via the Arma3 launcher as loacal addon. Then started the game with Alive and the addons i juat made, when in editor i put down the ORBAT modelus in the map with a single unit and click start the secen as singleplayer. The game would loaded the ORBAT creator as usual, then in faction editor i found the new faction i just made, then open the unit editor and import all the units from file. After all units are loaded, export all the config and cfgpathes as usual, and you done, all vehicles would be appear with gunners normally after you create the PBO file.

I dont know how it works but it worked for me at least. I am using this method to creatd a lot of unit factions for my own usage since last Oct.

Has anyone found a way to fix this yet?

BlazenYmother said it. It works, but there are still vechicles from some mods which simply don't work. My guess is that you probably could find out the different seats in the specific configs and than manually add them into the autogen.hpp. Takes some work though.