It may be worth looking at eConnect over Web Services to see if it is more efficient for the sales orders you're integrating into Dynamics GP and resulting in a backed up queue during peak times, causing timeouts.
Another option(s) you can potentially look at is:
--Schedule the integrations to not run during peak hours, instead running them during off-business hours and/or maybe when users are at lunch, i.e. a slower part of the day.
--If the sales orders contain a large volume of total orders and/or number of items contained per order, in each integration run, you may look at breaking the integrations into smaller chunks, so, for example, instead of sending through 1000 sales orders in one shot, have it do 4 runs of 250 orders each, to see if that goes through more smoothly and not get backed up so much.
--Make sure users aren't posting in Dynamics GP the same time the integrations are being run, as the posting process sometimes locks several tables the integrations may also need, thus causing delays.
That being said, depending on the integration code being passed through Web Services to create the sales orders, you may already be using eConnect procedures to do so.
Let us know if you have any questions.
Thanks