Been a longtime fan of the mod but seeing your post forced me to make an account.
I have found a workaround for this issue:
When playing as the republic, I ran into the same issue and couldnt figure out how to fix it so I became frustrated and exited to the main menu. Instead of my most recent save being, well, most recent, it was actually my autosave. I loaded the autosave and it was for a land battle at kauron. I had no units, but as the republic I started out with the mercenary structure. I ended up winning the battle because the enemy (Empire) retreated, but the planet did not change to my control. I had never even visited or had vision of the planet either.
i too have had this same problem and i feel i know what causes it, having 2 many ships in orbit when you start a ground assult will cause this problem. when you reload the auto save it puts you on a random planet with no units. you can work round this by having fewer ships in orbit when you start a ground battle im guessing the ai could cause the same problem if it starts a ground assault with 2 many ships in orbit.
i dunno how hard it is but i have terrible trouble moving units around on some ground maps any way of spacing the points out a bit more or some other way of making it no so much of a struggle to find where i should be dropping the units. sometime i drag a unit to the box and i have to move it to the top corner of the box and other times its somewhere else in the unit placment box.
if you need any help with filling out the missing decriptions id be glad to help i have some time on my hands atm and would love to help with some peon stuff.
great mod btw.