As Tomas Takac said, the timeout in the Connection String is for the connection process only.
The correct way woudl be to use the
CommandTimeOut[
^] property in your code.
If you are using the Microsoft Data Access Application Block SqlHelper class then sqlhelper has been succeeded by DataBase and you can set the command timeout with DBCommand.SetCommandTimeout.
If you are using an older version (i.e. MS DAAB SqlHelper) then there are overrides on the FillDataSet method that take a command timeout parameter.
If you are using something else, then search using intellisense for something similar to "commandtimeout" in your 3rd party dll or contact the author/vendor.