Off the top of my head, try turning on ship movement animation in the game options. It's either in (crown_icon), Empire Options button to the right of that dialog, or (more likely) in the main menu, options button. I'll try looking for the ini line...
--edit:
Ok, it's in the file Settings.txt in the Data folder. If you're using a mod, you will want to change it in the mod folder's Data folder.
There is a line that says
Quote:
System Ship Movement Delay Milliseconds := 0
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If you open in notepad, just do Ctrl+F, enter Movement Delay, and it will find it. Change the 0 to something larger; 1000 would be one second, but it would likely take a little longer (especially if you turn on animation).