I'm not sure this is entirely relevant to your problem but...
certain sp's allow to set a "timeout" parameter as for example when using replication. in this case you can "force" the merge replication agent to use longer timeout periods by simply adding the parameter -QueryTimeOut nnn (where timeout nnn sequence is specified in seconds)
after the name and other parameters of the sp.
This can also be set for example with the BCP routine in Mssql although i can't recall how the parameter is called in the case of bcp.