I tried this a few weeks ago. Using IE I logged in using my cousins EC number and PIN. I was given the normal check-in options of change seat etc. At the same time I opened Netscape and logged in using my EC number and PIN. I received a message saying "Seat change not available". I figured that the system was unhappy with having the same PNR open and accesible by two different session. I logged out of my account and quickly did the seat change and concluded the check-in for my cousin. I logged back in with my EC number and PIN and was able to change my seat as normal.

I know this is not exactly the same as your issue but I suspect it has something to do with only one session being able to access a PNR at any one time.