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When you are using WebDirect it will be running the script on the server, rather than in the FileMaker Go/Pro client. You might be able to use the 'Perform Script on Server' script step when using FileMaker Go or Pro to have it run in the same way - depends on what the script is doing.... Also note that PSOS has an option to 'wait for completion' which you should consider.
hope this helps :-)
What does the script do? It could potentially be optimized further.
A basic understanding of WHAT is slowing down over the WAN connection (rather than running the operation on the server, as is the case with PSoS or WebDirect), would definitely help you be a better developer and lead to other performance gains in your system.