I had some success getting around this problem, not fixing it.
I added in Intuitive shipping app and it integrates with my shipstation and pulls the rates from shipstation. It is a pay program but it adds a lot of nice features and does not remove shipping options for my customers that it does not think are relevant like shipstation. But most importantly, I went from having 2-3 customers complaining every day about this error (when having shipstation deliver shipping rates at checkout) to no complaints at all (with having intuitive shipping pull raties from shipstation). I have been running Intuitive shipping for more than a week now without an error.