I would try and open a file locally from IV (that means you have a local copy) that VE says is not there, and check its Vault status, to make sure Vault and IV are seeing it properly, ie you don't have to "add files."
If it shows up in IV with the circle I would see what VE shows to see if VE updates properly. Next I would check it out from IV and see if VE shows that too, and then Undo checkout. I would also try checking out from VE and see if they link up that way, and then undo checkout.
Screen caps would be helpful for this as well, to show the miss-matches.
Pete