After taking a new colony, it is important to change the suppression settings. The reason being, is that for some reason they don't like being your biotch, they decide to up rise against you, you will not loose troops that are not very effective.
Click on colony on side panel
Click on suppression setting tab on the colony window
Change the following to 0%;
Worker, Scouts, Transporters
*I personally also set Calvary and Cataphracts to 0%, they are much better at attacking
Make sure to save changes, this can be done once daily.