Unfortunately, I have no experience with VCD files, but I know they are not created in Encounter. One is not required for power analysis - you can do a vectorless analysis, but if you still want to use a VCD file, I would suggest posting the question in the Logic Design forum.
For your IOs - is this a chip or a block? Meaning, are you talking about actual IO pad cells, or IO pins? I'm guessing you've already zoomed in really close to make sure they're just not too small to show up when the whole design is fit to the Encounter window. Another thing to try is use the Design Browser to find one of your IO cells and select it, then hit Q to bring up the attributes form. Then you can see what coordinates the cell is placed at, and go to those coordinates for a look. Also try turning on all the objects and looking at the design in all 3 modes - floorplan, amoeba, and physical. This is a hard one to diagnose without having your design in front of me, but hopefully some of these suggestions will help.