[TNZ]

Try checking the AI settings files to see if the size of your colony ships is to big for the “Max Ship Size Tonnage From Start”entries. Also I had that problem with colony ships to, so I decided to do this:

AI Design Creation File:
Name := Colony (Rock)
Design Type := Colony (Rock)
Vehicle Type := Ship
Default Strategy := Don't Get Hurt
Size Minimum Tonnage := 250
Size Maximum Tonnage := 250
Num Must Have At Least 1 Ability := 1
Must Have Ability 1 := Colonize Planet - Rock
Majority Comp Spaces Per One := 10000
Majority Comp Ability := Weapon
Secondary Comp Spaces Per One := 10000
Secondary Comp Ability := Weapon

Vehicle Size File:
Colony Ship
Requirement Pct Colony Mods := 0