In the opening Cutscene, a marine tells the cheif that his armor is in "partial lock down." Meaning that parts of your armor won't work now. To fix this problem, you have to go to Crows Nest to get it fixed.
The second mission, the cheif enters Crows Nest. There, before he enters the ops center, he gets his armor fixed and it's there, your armor appears that you have earned on you after a quick black out, then you appear in the new armor you have earned.
[Edited on 08.14.2010 9:09 AM PDT]