I have some aliens rampaging through the Sol system shooting up mining colonies. I've ordered my warships that were orbiting Earth to move to engage, but the order has the phase "awaiting acknowledgment". They will not move, and I can't find a way to kick start them.
You are playing with the "Inexperienced Fleets" option. Each ship has a Task Force Training rating which is shown on the far right column of the ship information on the F12 window. It ranges from zero to 100%. This is the ability of that ship to work with other ships in a fleet and respond quickly to orders. It only comes into play when there are hostile contacts in the same system. A task group has a Task Force Training Rating that is equal to the average of all its ships. A low TF Training Rating means that task groups may take up to a minute or so to respond to movement commands. A low individual rating for a ship means it may take a while to open fire while told to do so and make have further delays when ordered to change targets. It will also be bad at formation keeping if you have a formation set up. This TF training rating represents the likely confusion when a group of ships that are not used to operate together are given orders to do something together in a stressful situation.
You can raise the TF training rating by sending your ships on Fleet Training Exercises, much like modern day navies do before deploying a fleet. This can be set on the second tab of the F12 window, near the bottom left. This will only work if the task group is in the same system as the Task Force to which it is assigned. The rate at which TF training points are gained is based on the crew training rating of the Task Force Commander and his Operations officer, plus a modifier from the ship commander based on his crew training rating.
if all of this sounds like more detail than you want, you can turn off the Inexperienced Fleet option on the Game window.
Then the SOB's are coasting through my active sensor range and I have more detail on them but my fire controls are not registering them as targets to launch missiles at. I'm sure it's something dumb I'm doing wrong. Any idea? 
Firstly check they are definitely active targets and not just thermal. If that is true, make sure your fire controls have the range to engage them. The ECM of enemy ships may also shorten your fire control range against them. You can counter this with ECCM or by getting closer.
Steve
