just re-read thread and it seems that he has tried all these things ... would like to know:

1) Has you tried configuring the login script from the user properites dialog itself, instead of from GPO's ?

2) Check which domain controller is authenticating you every time you login by echoing %logonsever%, it it always the same DC that is timing out ?

3) Still fuzzy in terms of what is starting and what is not. I think your hinting that kix32.exe is starting but is hanging, but is it finding and reading the script ?