Arnuz: Tried it in hot seat, there's still weirdness going on with the scV heroes. They attract other troops they don't need to go around and convert them. I've seen the karaghs from the 4square town move to the hero who had already moved to the closest tower. I'm guessing that the troops then convert the hero AI as he's not recruitable. Perhaps for this reason the hero becomes unrecruitable. Then even if other troops join - from a recruitable town - the stack becomes recruitable... But not the hero!
It'd seem that the hero moves to the closest tower and the troops then move to the hero. I've seen this happen both with the manually placed troops set to fortify and the auto-generated ones from the garrison. I've tried moving the hero to the tower but the same happens. Guessing that to be 100% sure you need to place the hero trapped somehow, maybe on an island close to an empty shipyard? Watch out for the lizards though that's not enough with them.
When I try it in SP I have no issues with any of the 5 heroes (using cheats to see them all). They're staying put like they should now.