Currently there is a 60 second timeout on all script executions for SCO deployment. I have run into situations where indexes on large data sets or table rebuilds on large tables exceeds that time frame resulting in SCO prematurely exiting the script deployment. The recommendation was to invest in better hardware. Unfortunately, better hardware cannot solve this problem where large data sets are in play. Having the ability to adjust the timeout default could help avoid such situations.

See for reference issue: http://redgatesupport.red-gate.com/requests/16832