I got the patcher to work after fiddling about with it a little. Originallly 1280x960 did not appear but I then set it to 1440x900 and that patched fine. EAX has been enabled with no problems (even if I don't know what it does exactly).
The loading bar lockup seems to be a common problem for many TSL players but I do not believe anyone knows exactly why it happens, not even the support staff at lucasarts...
Regarding mods. I have none installed currently as I wanted to get the game running properly first, otherwise it would be even harder to narrow down the reason. Read over the 'how to' threads and installing seems rather straightforward (yes I always read the read me).
Partial good news. After all the changes and tweaks I finally got it to run but on my main profile. I created a new profile (simply called test) and the game runs fine. I can start a new file, load both autosaves and regular. Not sure why though. Any ideas?