Bumping this thread to add some info.
I received the "logged in from another terminal" message many hours after logging in. I was booted from FFXI, but POL didn't log me out entirely. I was able to log back in immediately. My fiance was playing at the same time, and nothing happened to her. However, we're both linked to the same SE Account and use the same security token.
So, nothing happened to my character. I use Firefox with up-to-date Adblock and NoScript with IFRAMEs disabled and all that, have scanned and am currently thoroughly scanning for any trojan/keylogger activity. I was using FFXIAH when it occured, scripts temporarily disabled (only way to view Price History).
It would stand to reason that if I were actually compromised, they should've also been able to access the SE Account to change information, but they didn't. My fiance logged onto the SE Account from her computer and changed the password, and I'm going to change my POL ID password on her computer immediately as I perform scans on my own.
Just adding to the circumstantial info we have thus far. I think there's some merit in the theory presented by some that the hackers may not be attacking all of their victimss directly with malicious software, but rather have gained access to registration server information through some kind of leak. I haven't managed to turn up any signs of infection on my PC, but if I do, I'll post my findings here.