RE: Final nail in the coffen for Family Tables Intralink 3.3WF1.
OK - I answered my own question, the solution is kind of weird too.
One thing that did change is my Workstation - still the same build and configs. For some reason, when I start Pro/E from Intralink, Pro/E would pop up the Intralink log-in box and the Intralink Process not found error. Weird that I didn't notice this which proves if you throw up a lot of useless dialog boxes (see save layer status), you're very likely to miss ones that are important. I didn't clue into Pro/E not knowing where Intralink was.
When I checked the PTCSetup - everything looked ok and the Intralink folder/command was specified correctly from IT. I just re-selected the Intralink folder and after the set up finished, Pro does not ask for Intralink login. Nothing changed in the set-up, seems like just running it refreshed the .bat file perhaps?