[Parasite]

Watch the battle replay to give you a better idea what is happening. If the transport ships never make the run to the planet, you know more where the fault is. If they make a run to an unguarded planet, capture it, then have the still undestroyed enemies glass your new planet, you could have a different problem. I have also had a few times where a wall formation has prevented the transports from getting through to the planet. If the troop transports have guns, they can head toward the planet firing, glassing it before they get there.

The cargo carrying ships must be made as type "Troop Transport". At least I have not had problems if this is the case. this can not be changed on the fly like strategy can, but must have a ship designed that way (and then maybe have an existing ship retrofitted to that design.