Ok,
After some mucking around, I managed to get my ATC window back, with no Mission Pointers or Objectives (Stupid General and his sore back .. )
I deleted all the other flights under c:....\Microsoft Flight Simulator X\Flights\Other
except for
FLTSIM.FLT and
FLTSIM.WX
When you restart FSX it says it can not find the old default file, and will then look for the original file.
This will then put you back to the start.
Keep a copy of the other files before you delete them in case it does not work in your particular circumstance.
I hope that this helps a few people out.
Thanks.