About 90 percent of the time, this problem has to do with some element of TCP/IP connectivity. It can be server hardware, infrastructure hardware, DNS, and a host of other problems, but it is rarely a problem with SQL Server even though that is where the symptom appears.
It finishes most of the queries in the script, but on some (and not always the same tables) it gives the time out error. I am not quit sure where or how to research this problem.
Any ideas are welcome!
Is it the same server(s) every time ? If not, I think the source may be as Pat said, the network, etc. or the source script itself. Were there any changes/updates ? Security changes, patches applied , etc.