There are two places to update when increasing the length of script timeouts. Firstly, within the application itself, so that BSI knows it should wait longer for the job to finish.
The Script timeout parameter is found in the BSI user interface under the ‘Administration’ Tab -> Site Settings -> Advanced -> ’Calculation Engine’ folder -> ’Script timeout’ parameter
Secondly, IIS itself needs to be configured to avoid a timeout within the web server. Instructions for performing this are on Microsoft's site in KB268364:
The exact location of the setting varies between releases of IIS.
For IIS 6.0 / Windows Server 2003: -> Go to BSI Web-Site -> Choose 'Properties' -> 'Home Directory' Tab -> 'Configuration...' Button -> 'Options' Tab -> In the 'Application configuration' section increase the 'ASP script timeout' as required.
On Windows Server 2008: IIS Manager -> (on the left-hand side) click on Machine Name -> (on the right-hand side) within the ‘IIS’ Section -> click on ‘ASP’ -> within the ‘Limits Properties’ sub-section -> set ‘Script Time-out’ as required.