I'm having the exact same problem, but haven't tried anything to fix it as of yet. It goes to the cutscenes just fine, and plays them, but when it gets to the moment where the game would transition from the video back to regular gameplay, CRASH. Since you tried one solution and it wasn't a complete fix, and you haven't posted since... did you ever get the problem fixed completely? Any advice? (Hopefully someone has some simple advice?)
Another note - after I installed the game, the font on my computer changed for some reason. It's weird, and a little alarming - like installation downgraded the appearance of system fonts or something strange. I'm far from a computer expert, so maybe it's nothing, but it's odd.
EDIT: That text problem was fixed - apparently the installation turned off "clear text" or at least checking that setting made it right somehow. Huh.
This game, while I think is great, is the only game in the GOG catalog that I have that gave me the biggest headache. The font thing happens to me also, but only after exiting the game.
This game really needs to be fixed, but I don't know how much of that is in GOG's hands or Funcom's.
As far as crashes are concerned, mine runs pretty stable, only crashing at the police station (Win 8.1, Nvidia GeForce GTX 670). It crashed endlessly when I played around with the graphic settings via Nvidia control panel until I found a setting that would work (Antialiasing - FXAA On).
I don't know if it any help, but check out this forum (if you already haven't found it): http://forums.longestjourney.com/forumdisplay.php?f=13
You might find some useful information.