I have the same problem with one of my scripts.
In my application, I'm updating a series of database tables -- replacing the data from one database to another. Then, with one of the tables, I'm updating a field depending on some other data within that table.
When I run this script on my development system, there is no problem: The routine takes about 7 seconds in total. When I load the program onto my client's machines, it runs very slow and eventually times out as above.
I've broken the procedure down into smaller chunks which seems to solve the problem, but I'd really be interested in other possible solutions, including some way to remotely set the Server.ScriptTimeout (because I do not have access to the IIS Admin Tools for these applications).