The problem is, the only "challenge" I'm getting from this is having to move to colonize the planets over and over. I am allied with the rebels so they do not attack any ships or structures, rather they just jump into the planets gravity well, remove control, and then continue to sit there and to absolutely nothing. So far its happened about 6 times to 2 different planets, seems to have toned down now.

Sure, heres one of the planet: 

And one of the ships: 

Alright, that explains it. But why do the rebels just sit there? They seem to be pilling up and the only thing its causing me is annoyance and a small drop in performance when I zoom in on the planet.

Ah, alright. Seems to have stopped for the time being, thanks for clearing that up.

There's a chance of rebellion on any world that drops to 30% Alliegiance or less as a result of enemy culture. 

That's not entirely true Yarlen, personally I find myself losing planets regardless of whether or or not there is enemy culture present, and sometimes my culture isn't even below 30%.

Is there another event which also causes you to lose control of planets aside from partisans?

That would be the Open Rebellion event instead of the partisans event.

The game spams open Rebellions to the last known capital of a faction which has been defeated, no matter what you do, I find it so annoying that I just skip the last capital of any civilization entirely, I only plop a starbase there after destroying the system.

Probably should be tweaked, I imagine TEC Rebel players would love it in Multiplayer, assuming any games are played with Random Events on.

Well, someone loves it in MP...but that someone is usually whoever gets their titan there first for feeding, and that someone may or may not be on your team...

Hmmm, I've been looking in the RandomEventDefs file to see if I could tweak it a little, this is what we have currently:

randomEventDef
id "OPENREBELLION"
nameID "IDS_RANDOMEVENT_OPENREBELLION_NAME"
warningID "IDS_GAMEMESSAGE_RANDOMEVENTDETECTED"
spawnType "BuffAtLocation"
spawnEntity "RandomEventOpenRebellion"
playerOwnerType "Rebel"
spawnLocation "TriggerLocation"
excludedSpawnLocationCount 0
spawnRequirement "TriggerLowAllegiance"
triggerWeight 0.1
spawnWeight 1.0

I'm looking at reducing the frequency that this event occurs as well as possibly lowering the maximum (minimum?) allegiance requirement, I assumed the trigger weight would be related to the allegiance level, but 0.1? Make sense to anyone else?

Also I assume that by reducing the spawn weight the event will happen less often, haven't tested yet but I'll post results when I do.

Ah ok, derp, I didn't see that initially, thanks.

On another note it seems the spawn weight is the % chance that any particular event will occur when its trigger condition is met, which for most of them is a simple random timer between 300 and 1200 seconds. However in the case of 'Partisans' the chance is based on the trigger weight, which is 0.25 or 25%, and the chance is recalculated every 240 seconds that any given planet is close to being flipped by enemy culture.

The same seems to be true of 'Open Rebellion', with a trigger weight of only 0.1 or 10% the effect happens much less often, but as long as your planets are under the 30% threshold it's going to happen eventually.

So in conclusion the only way to stave off 'Partisans' is make sure there is no enemy culture affecting your planets, a difficult feat on the front lines at times; but there isn't really much you can do about 'Open Rebellion' if you can't get your allegiance above 30%, This isn't that big a deal for most players, but if you play on custom maps with many colonized militia planets like I do, build media hubs, broadcast centres or temples of communion at regular intervals to keep your culture above 30%.

The devs said it will be changed somehow in a future patch.