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Nothing is more fustrating than to worry your fledgling empire up to 11 or so colonies and then 4 of them break off... Happening routinely to me nowadays, how can I stop this? Even tried a game at full auto and it still happened.

Any help would be appreciated!

What is causing the rebellions in your case? When you look at the happiness of your colonies, what are the modifiers? What race/government combination are you playing?

Invading an independant colony of the same race as one of your alien colonies is a pretty sure fire way to incite a rebellion.

Lack of Intelligence Defense is also a main culprit, which the AI will make you sorry for neglecting. Make sure you have some seasoned agents on counter-intel.

Mosttimes my colonies rebels when i start them in systems with more then 1 other empire colonies.

You can try to set the Tax to 0, but to keep them at 0 you need to turn of the Tax automation.
Build fast a small Starport or Starbase with Medical/Recreation center.

But when you got the rebelation warning mosttimes its to late to do anything against it. You should sell that colony to the empire you share the system.

To avoid your Colonies at other empire system, you can disable that at the Options.